Browse Source

This is a test

p280381-featureCounts-1
Corneel Vermeulen 3 years ago
parent
commit
828476002a
  1. 131
      Tessa_sample_workflow/DESeq2_example.Rmd
  2. 422
      Tessa_sample_workflow/DESeq2_example.html
  3. 233
      Tessa_sample_workflow/db.csv
  4. 184
      Tessa_sample_workflow/rnaseqids_qc4_pass_plusref2.txt
  5. 1001
      Tessa_sample_workflow/sample.htseq.txt.table

131
Tessa_sample_workflow/DESeq2_example.Rmd

@ -0,0 +1,131 @@ @@ -0,0 +1,131 @@
---
title: "Sample workflow DESeq2 for Tessa"
author: "Corneel Vermeulen"
date: "`r Sys.Date()`"
output: html_document
---
### GSK asthma remission project
Hoi Tesssa, Dit is een aangepaste versie van het tutorial script dat ik voor Ilse maakte, vanwege een [verandering in DESeq2 VERSION 1.16.0](# https://support.bioconductor.org/p/95695/). Omdat de orginele count table erg groot is gebruikt het script een miniatuur versie gemaakt van 1000 willekeurige features.
### Preliminaries
load all required packages
```{r load_packgs, warning=FALSE, message=FALSE}
library("DESeq2")
library("gplots")
```
### load data
Hier laad je de count table and de database respectievelijk. Je kunt hier evt. je werkmap instellen.
```{r setwd_dataload}
#setwd("/path/to/your/wd")
CT<-read.delim("sample.htseq.txt.table", header = TRUE, sep = "\t",
quote = "", fill = TRUE, comment.char = "")
db <-read.csv("db.csv",header=T,sep=";",dec=",")
```
### Prepare data
Dit is het lastigste stuk. De sample_IDs zijn gemangeld tijdens het verwerken van de samples en dat maakt het matchen aan de klinische data een tijdrovende klus.
```{r showids}
head(colnames(CT))
head(db$rnaseq.id)
```
Ik heb al wat werk verzet door in de db overal een "X" voor te plakken en alle streepjes te vervangen door underscores. Nu moeten we nog de ".htseq.txt" kwijtraken. Zie ook dat sommige samples "NORM" en anderen "NORM_" genoemd zijn. Verder zijn er meerdere controle samples. Veel lelijke code hier, en waarschijnlijk niet bruikbaar voor jou:
```{r prepdata}
colnames(CT)[1] <- ""
cn.CT <- colnames(CT)
cn.CT <- cn.CT[2:length(cn.CT)] #drop the empty first cell
cn.CT <- gsub(".htseq.txt", "", cn.CT) # remove the suffix
cn.CT <- gsub("NORM.{0,}", "NORM_", cn.CT) # add one trailing underscore
cn.all <- as.character(db$rnaseq.id)
idx <- match(cn.CT,cn.all) #match the clinical data to the correct samples
idx[which(is.na(idx))] <- which(cn.all == "X263_110_T04_90226") # multiple ref samples
coldata <- db[idx,]
rownames(coldata) <- cn.CT
countdata <- CT[,c(2:ncol(CT))]
rownames(countdata) <- CT[,1]
coldata$batch.extract[which(coldata$rnaseq.id == "X263_110_T04_90226")] <- seq(1:6)
coldata$batch.extract<-as.factor(coldata$batch.extract) #batch nrs are factor levels
```
### QC-filter
We gebruiken alleen samples die de QC doorstaan en de beste reference sample (#2).
```{r qcfilter, message=FALSE}
qc.pass <- scan("rnaseqids_qc4_pass_plusref2.txt", what = "character")
idx.qc.pass <- which(coldata$rnaseq.id %in% qc.pass)
idx.ref2 <- which(coldata$rnaseq.id == "X263_110_T04_90226" & coldata$batch.extract == 2)
idx.qc.pass <- c(idx.qc.pass,idx.ref2)
coldata <- coldata[idx.qc.pass,]
countdata <- countdata[,idx.qc.pass]
colnames(countdata) <- NULL # fixes error
```
### Exploratory analysis
Nu we onze data klaar hebben, wordt alles veel eenvoudiger: We converteren onze count table naar een DESeqDataSet. We geven nog geen model op.
```{r convert}
dds <- DESeqDataSetFromMatrix(countData = countdata,
colData = coldata,
design = ~ 1)
```
Dan kijken we in een PCA of onze dataset zich gedraagt. Het is noodzakelijk de ruwe count data te transformeren daarvoor. Omdat we teveel samples hebben om een rlog transformatie te doen gebruiken we een [trucje](https://support.bioconductor.org/p/77122/).
```{r pca, message = FALSE}
dds <- estimateSizeFactors(dds)
baseMean <- rowMeans(counts(dds, normalized=TRUE))
idx.sub <- sample(which(baseMean > 5), 100)
dds.sub <- dds[idx.sub, ]
dds.sub <- estimateDispersions(dds.sub)
dispersionFunction(dds) <- dispersionFunction(dds.sub)
vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
plotPCA(vsd, intgroup = "gender")
```
### Differential expression
Tenslotte het echte werk. We voeren ons model in en creeren een nieuwe DESeqDataSet (de oude wordt daarbij overschreven). Dan testen we of er een overall verschil is tussen de levels van asthma. Vervolgens kijken we naar een specifiek contrast.
```{r difexp, message = FALSE}
dds <- DESeqDataSetFromMatrix(countData = countdata,
colData = coldata,
design = ~ gender + asthma.ics)
# Overall test (takes long time to run)
dds <- DESeq(dds, test="LRT", full=~ gender + asthma.ics, reduced=~ gender)
res <- results(dds)
res$symbol <- mcols(dds)$symbol
head(res[order(res$pvalue),],4)
summary(res)
sum(res$padj < 0.05, na.rm=T)
topGene <- rownames(res)[which.min(res$padj)]
plotCounts(dds, gene=topGene, intgroup=c("asthma.ics"))
```
Het feature met de meeste variatie tussen de groepen is `r topGene`, maar waarschijnlijk ben je geinteresseerd in een specifiek contrast, bijvoorbeeld asthma versus healthy:
```{r contrast}
dds.wald <- DESeq(dds, test="Wald", betaPrior = TRUE)
res.c <- results(dds.wald, contrast = c("asthma.ics","PersA_no_ICS","H"))
topGene.c <- rownames(res.c)[which.min(res.c$padj)]
```
Het feature dat het meest verschillend tot expressie komt in dit contrast is `r topGene.c`. Hierna zul je zelf je weg moeten vinden. Meer informatie vind je [hier](http://www.bioconductor.org/help/workflows/rnaseqGene/) en [hier](https://www.bioconductor.org/help/course-materials/2015/LearnBioconductorFeb2015/B02.1.1_RNASeqLab.html).
## session info
Packages used
```{r sessionInfo, include=TRUE, echo=TRUE, results='markup'}
sessionInfo()
```

422
Tessa_sample_workflow/DESeq2_example.html

File diff suppressed because one or more lines are too long

233
Tessa_sample_workflow/db.csv

@ -0,0 +1,233 @@ @@ -0,0 +1,233 @@
"rnaseq.id";"batch.extract";"gender";"asthma.ics";"age";"currentsmoking"
"X9_0_T06_90304";1;"male";"PersA_ICS";48,29021;"nonsmoker"
"X613_0_T07_90064";1;"female";"PersA_ICS";53,6783;"nonsmoker"
"X377_0_T06_90091";1;"male";"PersA_ICS";67,27995;"nonsmoker"
"X535_0_T07_90052";2;"female";"PersA_ICS";37,57974;"nonsmoker"
"X433_0_T06_90135";2;"female";"PersA_ICS";50,78702;"nonsmoker"
"X25_0_T06_90258";2;"female";"PersA_ICS";45,77949;"nonsmoker"
"X504_0_T07_90051";2;"male";"ClinR";52,11773;"nonsmoker"
"X545_0_T07_90061";2;"female";"PersA_ICS";36,43806;"nonsmoker"
"X440_0_T06_90072";3;"female";"PersA_no_ICS";55,91239;"nonsmoker"
"X615_0_T06_90136";3;"male";"PersA_ICS";39,42505;"nonsmoker"
"X1406_0_T04_90217";3;"female";"ClinR";63,5373;"smoker"
"X527_0_T07_90029";3;"male";"ClinR";45,21287;"nonsmoker"
"X451_0_T06_90027";4;"male";"PersA_ICS";39,8987;"nonsmoker"
"X543_0_T06_90110";4;"male";"PersA_ICS";25,10609;"smoker"
"X436_0_T06_90160";4;"male";"PersA_ICS";58,0916;"nonsmoker"
"X699_0_T06_90067";4;"female";"PersA_no_ICS";27,38946;"nonsmoker"
"X650_0_T06_90058";5;"female";"PersA_ICS";54,59001;"nonsmoker"
"X1417_0_T06_90320";5;"female";"PersA_ICS";56,31485;"nonsmoker"
"X636_0_T07_90028";5;"male";"PersA_no_ICS";52,3614;"smoker"
"X1317_0_T03_90195";6;"female";"ComR";55,6029;"nonsmoker"
"X434_0_T06_90088";6;"male";"PersA_ICS";36,01643;"smoker"
"X1408_0_T04_90132";6;"female";"PersA_no_ICS";60,64351;"nonsmoker"
"X70_0_T06_90296";6;"male";"ClinR";51,11567;"smoker"
"X51_0_T06_90222";6;"male";"PersA_ICS";46,23397;"nonsmoker"
"X1322_0_T04_90118";7;"male";"PersA_no_ICS";44,39687;"nonsmoker"
"X1319_0_T03_90187";7;"female";"ComR";66,5762;"nonsmoker"
"X454_0_T06_90220";7;"female";"PersA_ICS";50,48038;"nonsmoker"
"X1503_0_T06_90169";7;"male";"PersA_no_ICS";49,46201;"smoker"
"X67_0_T06_90307";7;"male";"PersA_no_ICS";52,45722;"smoker"
"X66_0_T06_90281";7;"male";"PersA_no_ICS";50,14089;"smoker"
"X1405_0_T04_90245";8;"male";"ClinR";65,5632;"nonsmoker"
"X530_0_T07_90019";8;"male";"PersA_ICS";49,43737;"nonsmoker"
"X1403_0_T04_90220";8;"male";"ClinR";60,54746;"nonsmoker"
"X1320_0_T03_90210";8;"male";"ComR";67,54814;"nonsmoker"
"X550_0_T07_90049";8;"male";"PersA_ICS";35,46886;"nonsmoker"
"X662_0_T06_90096";9;"female";"PersA_ICS";40,282;"nonsmoker"
"X450_0_T06_90202";9;"female";"ClinR";50,71857;"nonsmoker"
"X721_0_T06_90219";9;"female";"PersA_ICS";28,93087;"smoker"
"X464_0_T06_90221";9;"female";"PersA_ICS";54,56251;"nonsmoker"
"X728_0_T06_90052";10;"male";"PersA_ICS";38,42026;"smoker"
"X641_0_T06_90063";10;"male";"PersA_ICS";49,27858;"nonsmoker"
"X423_0_T06_90237";10;"female";"PersA_ICS";33,01289;"smoker"
"X33_0_T07_90020";10;"male";"PersA_ICS";50,26146;"nonsmoker"
"X1323_0_T04_90114";11;"male";"ClinR";46,53514;"nonsmoker"
"X496_0_T06_90319";11;"female";"PersA_ICS";30,31348;"nonsmoker"
"X1327_0_T05_90074";12;"male";"PersA_no_ICS";46,46943;"nonsmoker"
"X730_0_T06_90064";12;"female";"PersA_ICS";49,56879;"nonsmoker"
"X518_0_T06_90188";12;"female";"PersA_ICS";38,98688;"smoker"
"X466_0_T06_90045";12;"male";"PersA_no_ICS";38,90486;"nonsmoker"
"X413_0_T06_90159";13;"female";"PersA_no_ICS";52,77744;"nonsmoker"
"X460_0_T06_90266";13;"female";"PersA_ICS";28,62685;"nonsmoker"
"X419_0_T06_90175";13;"female";"PersA_ICS";54,72952;"nonsmoker"
"X642_0_T07_90030";13;"female";"ClinR";46,2204;"nonsmoker"
"X749_0_T06_90080";13;"male";"PersA_ICS";46,89665;"nonsmoker"
"X1502_0_T05_90096";14;"male";"PersA_no_ICS";63,83025;"nonsmoker"
"X1404_0_T04_90182";15;"male";"PersA_no_ICS";47,21686;"nonsmoker"
"X1504_0_T06_90174";15;"female";"PersA_ICS";53,50297;"nonsmoker"
"X378_0_T06_90242";15;"male";"PersA_ICS";40,24903;"nonsmoker"
"X1410_0_T05_90120";15;"male";"ComR";49,2593;"nonsmoker"
"X13_0_T06_90295";16;"male";"PersA_ICS";52,12594;"nonsmoker"
"X1402_0_T05_90007";16;"male";"PersA_ICS";59,44444;"smoker"
"X304_0_T06_90224";17;"male";"PersA_no_ICS";50,74595;"smoker"
"X1413_0_T07_90004";17;"female";"PersA_ICS";35,98905;"nonsmoker"
"X658_0_T06_90150";17;"female";"PersA_no_ICS";35,15663;"nonsmoker"
"X478_0_T06_90151";17;"female";"ClinR";41,07039;"nonsmoker"
"X1401_0_T04_90183";17;"male";"ComR";64,92802;"smoker"
"X1412_0_T06_90303";18;"female";"PersA_ICS";64,76397;"smoker"
"X632_0_T07_90050";18;"female";"PersA_ICS";54,48871;"nonsmoker"
"X353_0_T06_90035";18;"male";"PersA_ICS";51,76181;"nonsmoker"
"X399_0_T06_90196";18;"female";"PersA_ICS";49,76306;"nonsmoker"
"X1411_0_T06_90006";18;"female";"ClinR";58,63119;"smoker"
"X1505_0_T07_90037";19;"female";"PersA_ICS";40,05202;"nonsmoker"
"X742_0_T06_90069";19;"male";"PersA_ICS";35,04997;"nonsmoker"
"X695_0_T06_90053";19;"female";"ComR";28,61054;"nonsmoker"
"X391_0_T06_90238";20;"male";"PersA_ICS";59,41399;"nonsmoker"
"X1415_0_T07_90003";20;"male";"PersA_ICS";53,70021;"nonsmoker"
"X474_0_T06_90079";20;"female";"PersA_no_ICS";28,57495;"nonsmoker"
"X487_1_T04_90142";18;"male";"PersA_no_ICS";38,65834;"nonsmoker"
"X124_11_T05_90014";5;"male";"PersA_no_ICS";64,27116;"smoker"
"X80_11_T04_90157";7;"female";"ClinR";71,6823;"nonsmoker"
"X7_21_T04_90179";1;"female";"ClinR";42,68846;"nonsmoker"
"X57_21_T05_90106";5;"male";"ClinR";47,85478;"nonsmoker"
"X175_21_T05_90105";19;"female";"ClinR";60,01369;"nonsmoker"
"X195_22_T04_90096";8;"male";"ClinR";40,93623;"nonsmoker"
"X53_22_T04_90131";10;"male";"ClinR";38,84999;"nonsmoker"
"X22_27_T04_90144";13;"female";"ClinR";45,59879;"nonsmoker"
"X108_110_T05_90051";1;"male";"ComR";51,54552;"smoker"
"X98_110_T02_10430";1;"male";"ClinR";63,19496;"nonsmoker"
"X77_110_T05_90091";2;"male";"PersA_ICS";67,51255;"nonsmoker"
"X154_110_T05_90071";2;"male";"PersA_ICS";56,34486;"nonsmoker"
"X37_110_T06_90046";3;"female";"PersA_ICS";71,83288;"nonsmoker"
"X99_110_T05_90056";4;"female";"PersA_ICS";60,25724;"nonsmoker"
"X54_110_T05_90052";4;"male";"PersA_no_ICS";53,10598;"smoker"
"X33_110_T02_12543";4;"male";"PersA_no_ICS";48,3914;"nonsmoker"
"X107_110_T05_90025";5;"female";"PersA_ICS";49,56046;"nonsmoker"
"X111_110_T02_11651";5;"male";"ClinR";49,42083;"nonsmoker"
"X87_110_T06_90007";5;"female";"PersA_no_ICS";57,41832;"smoker"
"X112_110_T02_12285";6;"female";"ClinR";64,83767;"nonsmoker"
"X45_110_T02_10969";8;"female";"PersA_no_ICS";62,70214;"nonsmoker"
"X263_110_T04_90226";9;"male";"ComR";47,5235;"smoker"
"X181_110_T06_90019";9;"male";"PersA_ICS";61,94114;"nonsmoker"
"X132_110_T06_90009";11;"female";"PersA_ICS";61,55521;"nonsmoker"
"X50_110_T02_09087";11;"female";"ClinR";60,87064;"nonsmoker"
"X142_110_T06_90144";12;"male";"PersA_ICS";62,69667;"nonsmoker"
"X76_110_T02_09747";12;"female";"ComR";53,79055;"nonsmoker"
"X3_110_T05_90001";12;"female";"PersA_ICS";67,90965;"nonsmoker"
"X18_110_T05_90100";14;"male";"PersA_ICS";68,86505;"nonsmoker"
"X216_110_T03_90106";14;"male";"PersA_no_ICS";54,20112;"nonsmoker"
"X220_110_T04_90021";14;"male";"PersA_no_ICS";56,39995;"nonsmoker"
"X156_110_T05_90018";15;"male";"PersA_no_ICS";53,05407;"nonsmoker"
"X205_110_T04_90200";15;"male";"ClinR";51,37292;"nonsmoker"
"X183_110_T05_90090";15;"male";"PersA_ICS";50,08339;"nonsmoker"
"X176_110_T04_90246";16;"male";"ClinR";47,34018;"nonsmoker"
"X134_110_T04_90117";16;"female";"ClinR";57,44;"nonsmoker"
"X165_110_T05_90099";16;"male";"ClinR";58,34371;"smoker"
"X247_110_T02_07964";17;"male";"ComR";53,58236;"nonsmoker"
"X43_110_T05_90008";19;"female";"PersA_ICS";60,62434;"nonsmoker"
"X46_110_T05_90118";19;"female";"PersA_no_ICS";53,8152;"smoker"
"X9_210_T05_90023";1;"female";"ComR";48,95003;"nonsmoker"
"X201_210_T04_90113";3;"female";"ComR";48,98551;"nonsmoker"
"X107_210_T05_90026";3;"female";"PersA_ICS";23,05533;"nonsmoker"
"X60_210_T06_90065";6;"female";"ClinR";25,41832;"smoker"
"X108_210_T05_90062";9;"female";"ClinR";25,96566;"nonsmoker"
"X189_210_T05_90054";15;"female";"PersA_no_ICS";29,55499;"nonsmoker"
"X133_210_T05_90109";18;"female";"PersA_no_ICS";30,4011;"nonsmoker"
"X175_210_T06_90034";18;"male";"ClinR";61,58259;"nonsmoker"
"X23_220_T05_90086";9;"male";"PersA_no_ICS";35,41125;"smoker"
"X133_220_T05_90110";10;"male";"ClinR";27,50171;"nonsmoker"
"X135_220_T04_90135";10;"female";"ClinR";46,13541;"nonsmoker"
"X149_220_T04_90146";14;"male";"ClinR";37,74663;"nonsmoker"
"X67_220_T05_90072";16;"female";"PersA_no_ICS";26,54609;"nonsmoker"
"X99_220_T05_90057";16;"female";"ComR";33,21275;"nonsmoker"
"X154_230_T05_90116";13;"male";"PersA_no_ICS";21,59902;"smoker"
"X195_311_T06_90020";11;"male";"ComR";19,71538;"smoker"
"X201_311_T06_90280";14;"female";"PersA_ICS";20,55841;"nonsmoker"
"X175_311_T05_90103";16;"female";"ClinR";25,77128;"nonsmoker"
"X172_311_T05_90061";19;"female";"PersA_no_ICS";22,40372;"smoker"
"X37_331_T05_90019";13;"female";"ComR";18,17112;"nonsmoker"
"X37_NORM_";1;"female";"H";20,11761;"nonsmoker"
"X84_NORM_";1;"male";"H";24,26831;"smoker"
"X71_NORM_";1;"female";"H";70,80071;"nonsmoker"
"X6_NORM_";1;"female";"H";51,05807;"smoker"
"X102_NORM_";1;"female";"H";20,38866;"smoker"
"X81_NORM_";2;"female";"H";37,17728;"nonsmoker"
"X111_NORM_";2;"male";"H";20,32569;"smoker"
"X30_NORM_";2;"male";"H";63,52373;"nonsmoker"
"X128_NORM_";2;"male";"H";45,20465;"smoker"
"X25_NORM_";2;"male";"H";19,3128;"nonsmoker"
"X163_NORM_";3;"male";"H";21,64556;"nonsmoker"
"X159_NORM_";3;"male";"H";27,44159;"smoker"
"X24_NORM_";3;"male";"H";70,4449;"nonsmoker"
"X47_NORM_";3;"male";"H";66,8501;"nonsmoker"
"X78_NORM_";3;"female";"H";19,89585;"nonsmoker"
"X85_NORM_";4;"male";"H";28,65423;"smoker"
"X122_NORM_";4;"male";"H";57,52213;"smoker"
"X39_NORM_";4;"female";"H";21,58784;"nonsmoker"
"X4_NORM_";4;"male";"H";73,03206;"nonsmoker"
"X28_NORM_";4;"male";"H";49,58236;"smoker"
"X46_NORM_";5;"female";"H";23,63028;"nonsmoker"
"X108_NORM_";5;"male";"H";19,77276;"smoker"
"X99_NORM_";5;"male";"H";64,15606;"smoker"
"X40_NORM_";5;"male";"H";58,31063;"nonsmoker"
"X88_NORM_";6;"male";"H";24,71469;"nonsmoker"
"X125_NORM_";6;"male";"H";37,85341;"smoker"
"X139_NORM_";6;"female";"H";46,49144;"smoker"
"X60_NORM_";6;"female";"H";55,9506;"nonsmoker"
"X105_NORM_";6;"female";"H";20,82957;"nonsmoker"
"X114_NORM_";7;"female";"H";22,88569;"nonsmoker"
"X135_NORM_";7;"female";"H";20,54768;"smoker"
"X77_NORM_";7;"male";"H";59,01711;"nonsmoker"
"X158_NORM_";7;"male";"H";52,01916;"smoker"
"X42_NORM_";7;"female";"H";23,90691;"nonsmoker"
"X147_NORM_";8;"female";"H";22,84189;"smoker"
"X98_NORM_";8;"female";"H";42,987;"smoker"
"X124_NORM_";8;"male";"H";25,13895;"nonsmoker"
"X1_NORM_";8;"male";"H";65,48106;"nonsmoker"
"X115_NORM_";8;"female";"H";20,38319;"smoker"
"X164_NORM_";9;"female";"H";23,25816;"smoker"
"X146_NORM_";9;"female";"H";21,58807;"nonsmoker"
"X113_NORM_";9;"male";"H";40,52008;"smoker"
"X23_NORM_";9;"male";"H";65,95483;"nonsmoker"
"X153_NORM_";10;"female";"H";34,09719;"nonsmoker"
"X17_NORM_";10;"female";"H";23,63324;"smoker"
"X8_NORM_";10;"male";"H";49,48654;"nonsmoker"
"X34_NORM_";10;"male";"H";53,90828;"nonsmoker"
"X48_NORM_";10;"female";"H";45,47285;"nonsmoker"
"X154_NORM_";11;"female";"H";20,06571;"nonsmoker"
"X166_NORM_";11;"male";"H";58,31896;"smoker"
"X10_NORM_";11;"male";"H";66,11088;"nonsmoker"
"X86_NORM_";11;"male";"H";55,93155;"smoker"
"X68_NORM_";11;"female";"H";46,40372;"nonsmoker"
"X49_NORM_";11;"male";"H";48,9554;"nonsmoker"
"X22_NORM_";11;"male";"H";58,02875;"smoker"
"X161_NORM_";12;"male";"H";21,21024;"nonsmoker"
"X20_NORM_";12;"male";"H";19,18138;"nonsmoker"
"X15_NORM_";12;"male";"H";69,07335;"nonsmoker"
"X66_NORM_";12;"male";"H";70,61453;"smoker"
"X106_NORM_";12;"male";"H";20,38319;"smoker"
"X130_NORM_";13;"female";"H";29,31964;"smoker"
"X16_NORM_";13;"male";"H";57,41547;"nonsmoker"
"X18_NORM_";13;"female";"H";39,01711;"nonsmoker"
"X74_NORM_";13;"male";"H";57,6345;"nonsmoker"
"X31_NORM_";14;"female";"H";53,74401;"smoker"
"X32_NORM_";14;"male";"H";44,20808;"nonsmoker"
"X118_NORM_";14;"male";"H";22,5762;"smoker"
"X123_NORM_";14;"female";"H";58,97867;"smoker"
"X145_NORM_";14;"male";"H";46,35181;"smoker"
"X52_NORM_";14;"male";"H";19,09651;"nonsmoker"
"X116_NORM_";15;"male";"H";19,94798;"smoker"
"X41_NORM_";15;"female";"H";56,57757;"nonsmoker"
"X82_NORM_";15;"male";"H";57,96578;"nonsmoker"
"X57_NORM_";15;"female";"H";51,80276;"nonsmoker"
"X35_NORM_";16;"male";"H";35,5729;"smoker"
"X80_NORM_";16;"female";"H";56,37223;"smoker"
"X63_NORM_";16;"female";"H";45,18001;"nonsmoker"
"X61_NORM_";16;"female";"H";57,64271;"nonsmoker"
"X92_NORM_";17;"female";"H";23,47445;"smoker"
"X136_NORM_";17;"male";"H";59,48517;"smoker"
"X89_NORM_";17;"female";"H";22,97057;"nonsmoker"
"X138_NORM_";17;"female";"H";43,02247;"smoker"
"X2_NORM_";17;"male";"H";47,92049;"smoker"
"X155_NORM_";17;"female";"H";18,43406;"nonsmoker"
"X96_NORM_";18;"female";"H";23,95083;"smoker"
"X137_NORM_";18;"male";"H";52,53103;"smoker"
"X104_NORM_";18;"male";"H";20,36676;"nonsmoker"
"X148_NORM_";18;"female";"H";41,40452;"smoker"
"X129_NORM_";19;"male";"H";21,76854;"nonsmoker"
"X149_NORM_";19;"male";"H";43,3128;"smoker"
"X101_NORM_";19;"male";"H";22,25314;"smoker"
"X33_NORM_";19;"female";"H";50,93771;"smoker"
"X109_NORM_";19;"male";"H";19,70694;"smoker"
"X55_NORM_";20;"male";"H";28,94456;"nonsmoker"
1 rnaseq.id batch.extract gender asthma.ics age currentsmoking
2 X9_0_T06_90304 1 male PersA_ICS 48,29021 nonsmoker
3 X613_0_T07_90064 1 female PersA_ICS 53,6783 nonsmoker
4 X377_0_T06_90091 1 male PersA_ICS 67,27995 nonsmoker
5 X535_0_T07_90052 2 female PersA_ICS 37,57974 nonsmoker
6 X433_0_T06_90135 2 female PersA_ICS 50,78702 nonsmoker
7 X25_0_T06_90258 2 female PersA_ICS 45,77949 nonsmoker
8 X504_0_T07_90051 2 male ClinR 52,11773 nonsmoker
9 X545_0_T07_90061 2 female PersA_ICS 36,43806 nonsmoker
10 X440_0_T06_90072 3 female PersA_no_ICS 55,91239 nonsmoker
11 X615_0_T06_90136 3 male PersA_ICS 39,42505 nonsmoker
12 X1406_0_T04_90217 3 female ClinR 63,5373 smoker
13 X527_0_T07_90029 3 male ClinR 45,21287 nonsmoker
14 X451_0_T06_90027 4 male PersA_ICS 39,8987 nonsmoker
15 X543_0_T06_90110 4 male PersA_ICS 25,10609 smoker
16 X436_0_T06_90160 4 male PersA_ICS 58,0916 nonsmoker
17 X699_0_T06_90067 4 female PersA_no_ICS 27,38946 nonsmoker
18 X650_0_T06_90058 5 female PersA_ICS 54,59001 nonsmoker
19 X1417_0_T06_90320 5 female PersA_ICS 56,31485 nonsmoker
20 X636_0_T07_90028 5 male PersA_no_ICS 52,3614 smoker
21 X1317_0_T03_90195 6 female ComR 55,6029 nonsmoker
22 X434_0_T06_90088 6 male PersA_ICS 36,01643 smoker
23 X1408_0_T04_90132 6 female PersA_no_ICS 60,64351 nonsmoker
24 X70_0_T06_90296 6 male ClinR 51,11567 smoker
25 X51_0_T06_90222 6 male PersA_ICS 46,23397 nonsmoker
26 X1322_0_T04_90118 7 male PersA_no_ICS 44,39687 nonsmoker
27 X1319_0_T03_90187 7 female ComR 66,5762 nonsmoker
28 X454_0_T06_90220 7 female PersA_ICS 50,48038 nonsmoker
29 X1503_0_T06_90169 7 male PersA_no_ICS 49,46201 smoker
30 X67_0_T06_90307 7 male PersA_no_ICS 52,45722 smoker
31 X66_0_T06_90281 7 male PersA_no_ICS 50,14089 smoker
32 X1405_0_T04_90245 8 male ClinR 65,5632 nonsmoker
33 X530_0_T07_90019 8 male PersA_ICS 49,43737 nonsmoker
34 X1403_0_T04_90220 8 male ClinR 60,54746 nonsmoker
35 X1320_0_T03_90210 8 male ComR 67,54814 nonsmoker
36 X550_0_T07_90049 8 male PersA_ICS 35,46886 nonsmoker
37 X662_0_T06_90096 9 female PersA_ICS 40,282 nonsmoker
38 X450_0_T06_90202 9 female ClinR 50,71857 nonsmoker
39 X721_0_T06_90219 9 female PersA_ICS 28,93087 smoker
40 X464_0_T06_90221 9 female PersA_ICS 54,56251 nonsmoker
41 X728_0_T06_90052 10 male PersA_ICS 38,42026 smoker
42 X641_0_T06_90063 10 male PersA_ICS 49,27858 nonsmoker
43 X423_0_T06_90237 10 female PersA_ICS 33,01289 smoker
44 X33_0_T07_90020 10 male PersA_ICS 50,26146 nonsmoker
45 X1323_0_T04_90114 11 male ClinR 46,53514 nonsmoker
46 X496_0_T06_90319 11 female PersA_ICS 30,31348 nonsmoker
47 X1327_0_T05_90074 12 male PersA_no_ICS 46,46943 nonsmoker
48 X730_0_T06_90064 12 female PersA_ICS 49,56879 nonsmoker
49 X518_0_T06_90188 12 female PersA_ICS 38,98688 smoker
50 X466_0_T06_90045 12 male PersA_no_ICS 38,90486 nonsmoker
51 X413_0_T06_90159 13 female PersA_no_ICS 52,77744 nonsmoker
52 X460_0_T06_90266 13 female PersA_ICS 28,62685 nonsmoker
53 X419_0_T06_90175 13 female PersA_ICS 54,72952 nonsmoker
54 X642_0_T07_90030 13 female ClinR 46,2204 nonsmoker
55 X749_0_T06_90080 13 male PersA_ICS 46,89665 nonsmoker
56 X1502_0_T05_90096 14 male PersA_no_ICS 63,83025 nonsmoker
57 X1404_0_T04_90182 15 male PersA_no_ICS 47,21686 nonsmoker
58 X1504_0_T06_90174 15 female PersA_ICS 53,50297 nonsmoker
59 X378_0_T06_90242 15 male PersA_ICS 40,24903 nonsmoker
60 X1410_0_T05_90120 15 male ComR 49,2593 nonsmoker
61 X13_0_T06_90295 16 male PersA_ICS 52,12594 nonsmoker
62 X1402_0_T05_90007 16 male PersA_ICS 59,44444 smoker
63 X304_0_T06_90224 17 male PersA_no_ICS 50,74595 smoker
64 X1413_0_T07_90004 17 female PersA_ICS 35,98905 nonsmoker
65 X658_0_T06_90150 17 female PersA_no_ICS 35,15663 nonsmoker
66 X478_0_T06_90151 17 female ClinR 41,07039 nonsmoker
67 X1401_0_T04_90183 17 male ComR 64,92802 smoker
68 X1412_0_T06_90303 18 female PersA_ICS 64,76397 smoker
69 X632_0_T07_90050 18 female PersA_ICS 54,48871 nonsmoker
70 X353_0_T06_90035 18 male PersA_ICS 51,76181 nonsmoker
71 X399_0_T06_90196 18 female PersA_ICS 49,76306 nonsmoker
72 X1411_0_T06_90006 18 female ClinR 58,63119 smoker
73 X1505_0_T07_90037 19 female PersA_ICS 40,05202 nonsmoker
74 X742_0_T06_90069 19 male PersA_ICS 35,04997 nonsmoker
75 X695_0_T06_90053 19 female ComR 28,61054 nonsmoker
76 X391_0_T06_90238 20 male PersA_ICS 59,41399 nonsmoker
77 X1415_0_T07_90003 20 male PersA_ICS 53,70021 nonsmoker
78 X474_0_T06_90079 20 female PersA_no_ICS 28,57495 nonsmoker
79 X487_1_T04_90142 18 male PersA_no_ICS 38,65834 nonsmoker
80 X124_11_T05_90014 5 male PersA_no_ICS 64,27116 smoker
81 X80_11_T04_90157 7 female ClinR 71,6823 nonsmoker
82 X7_21_T04_90179 1 female ClinR 42,68846 nonsmoker
83 X57_21_T05_90106 5 male ClinR 47,85478 nonsmoker
84 X175_21_T05_90105 19 female ClinR 60,01369 nonsmoker
85 X195_22_T04_90096 8 male ClinR 40,93623 nonsmoker
86 X53_22_T04_90131 10 male ClinR 38,84999 nonsmoker
87 X22_27_T04_90144 13 female ClinR 45,59879 nonsmoker
88 X108_110_T05_90051 1 male ComR 51,54552 smoker
89 X98_110_T02_10430 1 male ClinR 63,19496 nonsmoker
90 X77_110_T05_90091 2 male PersA_ICS 67,51255 nonsmoker
91 X154_110_T05_90071 2 male PersA_ICS 56,34486 nonsmoker
92 X37_110_T06_90046 3 female PersA_ICS 71,83288 nonsmoker
93 X99_110_T05_90056 4 female PersA_ICS 60,25724 nonsmoker
94 X54_110_T05_90052 4 male PersA_no_ICS 53,10598 smoker
95 X33_110_T02_12543 4 male PersA_no_ICS 48,3914 nonsmoker
96 X107_110_T05_90025 5 female PersA_ICS 49,56046 nonsmoker
97 X111_110_T02_11651 5 male ClinR 49,42083 nonsmoker
98 X87_110_T06_90007 5 female PersA_no_ICS 57,41832 smoker
99 X112_110_T02_12285 6 female ClinR 64,83767 nonsmoker
100 X45_110_T02_10969 8 female PersA_no_ICS 62,70214 nonsmoker
101 X263_110_T04_90226 9 male ComR 47,5235 smoker
102 X181_110_T06_90019 9 male PersA_ICS 61,94114 nonsmoker
103 X132_110_T06_90009 11 female PersA_ICS 61,55521 nonsmoker
104 X50_110_T02_09087 11 female ClinR 60,87064 nonsmoker
105 X142_110_T06_90144 12 male PersA_ICS 62,69667 nonsmoker
106 X76_110_T02_09747 12 female ComR 53,79055 nonsmoker
107 X3_110_T05_90001 12 female PersA_ICS 67,90965 nonsmoker
108 X18_110_T05_90100 14 male PersA_ICS 68,86505 nonsmoker
109 X216_110_T03_90106 14 male PersA_no_ICS 54,20112 nonsmoker
110 X220_110_T04_90021 14 male PersA_no_ICS 56,39995 nonsmoker
111 X156_110_T05_90018 15 male PersA_no_ICS 53,05407 nonsmoker
112 X205_110_T04_90200 15 male ClinR 51,37292 nonsmoker
113 X183_110_T05_90090 15 male PersA_ICS 50,08339 nonsmoker
114 X176_110_T04_90246 16 male ClinR 47,34018 nonsmoker
115 X134_110_T04_90117 16 female ClinR 57,44 nonsmoker
116 X165_110_T05_90099 16 male ClinR 58,34371 smoker
117 X247_110_T02_07964 17 male ComR 53,58236 nonsmoker
118 X43_110_T05_90008 19 female PersA_ICS 60,62434 nonsmoker
119 X46_110_T05_90118 19 female PersA_no_ICS 53,8152 smoker
120 X9_210_T05_90023 1 female ComR 48,95003 nonsmoker
121 X201_210_T04_90113 3 female ComR 48,98551 nonsmoker
122 X107_210_T05_90026 3 female PersA_ICS 23,05533 nonsmoker
123 X60_210_T06_90065 6 female ClinR 25,41832 smoker
124 X108_210_T05_90062 9 female ClinR 25,96566 nonsmoker
125 X189_210_T05_90054 15 female PersA_no_ICS 29,55499 nonsmoker
126 X133_210_T05_90109 18 female PersA_no_ICS 30,4011 nonsmoker
127 X175_210_T06_90034 18 male ClinR 61,58259 nonsmoker
128 X23_220_T05_90086 9 male PersA_no_ICS 35,41125 smoker
129 X133_220_T05_90110 10 male ClinR 27,50171 nonsmoker
130 X135_220_T04_90135 10 female ClinR 46,13541 nonsmoker
131 X149_220_T04_90146 14 male ClinR 37,74663 nonsmoker
132 X67_220_T05_90072 16 female PersA_no_ICS 26,54609 nonsmoker
133 X99_220_T05_90057 16 female ComR 33,21275 nonsmoker
134 X154_230_T05_90116 13 male PersA_no_ICS 21,59902 smoker
135 X195_311_T06_90020 11 male ComR 19,71538 smoker
136 X201_311_T06_90280 14 female PersA_ICS 20,55841 nonsmoker
137 X175_311_T05_90103 16 female ClinR 25,77128 nonsmoker
138 X172_311_T05_90061 19 female PersA_no_ICS 22,40372 smoker
139 X37_331_T05_90019 13 female ComR 18,17112 nonsmoker
140 X37_NORM_ 1 female H 20,11761 nonsmoker
141 X84_NORM_ 1 male H 24,26831 smoker
142 X71_NORM_ 1 female H 70,80071 nonsmoker
143 X6_NORM_ 1 female H 51,05807 smoker
144 X102_NORM_ 1 female H 20,38866 smoker
145 X81_NORM_ 2 female H 37,17728 nonsmoker
146 X111_NORM_ 2 male H 20,32569 smoker
147 X30_NORM_ 2 male H 63,52373 nonsmoker
148 X128_NORM_ 2 male H 45,20465 smoker
149 X25_NORM_ 2 male H 19,3128 nonsmoker
150 X163_NORM_ 3 male H 21,64556 nonsmoker
151 X159_NORM_ 3 male H 27,44159 smoker
152 X24_NORM_ 3 male H 70,4449 nonsmoker
153 X47_NORM_ 3 male H 66,8501 nonsmoker
154 X78_NORM_ 3 female H 19,89585 nonsmoker
155 X85_NORM_ 4 male H 28,65423 smoker
156 X122_NORM_ 4 male H 57,52213 smoker
157 X39_NORM_ 4 female H 21,58784 nonsmoker
158 X4_NORM_ 4 male H 73,03206 nonsmoker
159 X28_NORM_ 4 male H 49,58236 smoker
160 X46_NORM_ 5 female H 23,63028 nonsmoker
161 X108_NORM_ 5 male H 19,77276 smoker
162 X99_NORM_ 5 male H 64,15606 smoker
163 X40_NORM_ 5 male H 58,31063 nonsmoker
164 X88_NORM_ 6 male H 24,71469 nonsmoker
165 X125_NORM_ 6 male H 37,85341 smoker
166 X139_NORM_ 6 female H 46,49144 smoker
167 X60_NORM_ 6 female H 55,9506 nonsmoker
168 X105_NORM_ 6 female H 20,82957 nonsmoker
169 X114_NORM_ 7 female H 22,88569 nonsmoker
170 X135_NORM_ 7 female H 20,54768 smoker
171 X77_NORM_ 7 male H 59,01711 nonsmoker
172 X158_NORM_ 7 male H 52,01916 smoker
173 X42_NORM_ 7 female H 23,90691 nonsmoker
174 X147_NORM_ 8 female H 22,84189 smoker
175 X98_NORM_ 8 female H 42,987 smoker
176 X124_NORM_ 8 male H 25,13895 nonsmoker
177 X1_NORM_ 8 male H 65,48106 nonsmoker
178 X115_NORM_ 8 female H 20,38319 smoker
179 X164_NORM_ 9 female H 23,25816 smoker
180 X146_NORM_ 9 female H 21,58807 nonsmoker
181 X113_NORM_ 9 male H 40,52008 smoker
182 X23_NORM_ 9 male H 65,95483 nonsmoker
183 X153_NORM_ 10 female H 34,09719 nonsmoker
184 X17_NORM_ 10 female H 23,63324 smoker
185 X8_NORM_ 10 male H 49,48654 nonsmoker
186 X34_NORM_ 10 male H 53,90828 nonsmoker
187 X48_NORM_ 10 female H 45,47285 nonsmoker
188 X154_NORM_ 11 female H 20,06571 nonsmoker
189 X166_NORM_ 11 male H 58,31896 smoker
190 X10_NORM_ 11 male H 66,11088 nonsmoker
191 X86_NORM_ 11 male H 55,93155 smoker
192 X68_NORM_ 11 female H 46,40372 nonsmoker
193 X49_NORM_ 11 male H 48,9554 nonsmoker
194 X22_NORM_ 11 male H 58,02875 smoker
195 X161_NORM_ 12 male H 21,21024 nonsmoker
196 X20_NORM_ 12 male H 19,18138 nonsmoker
197 X15_NORM_ 12 male H 69,07335 nonsmoker
198 X66_NORM_ 12 male H 70,61453 smoker
199 X106_NORM_ 12 male H 20,38319 smoker
200 X130_NORM_ 13 female H 29,31964 smoker
201 X16_NORM_ 13 male H 57,41547 nonsmoker
202 X18_NORM_ 13 female H 39,01711 nonsmoker
203 X74_NORM_ 13 male H 57,6345 nonsmoker
204 X31_NORM_ 14 female H 53,74401 smoker
205 X32_NORM_ 14 male H 44,20808 nonsmoker
206 X118_NORM_ 14 male H 22,5762 smoker
207 X123_NORM_ 14 female H 58,97867 smoker
208 X145_NORM_ 14 male H 46,35181 smoker
209 X52_NORM_ 14 male H 19,09651 nonsmoker
210 X116_NORM_ 15 male H 19,94798 smoker
211 X41_NORM_ 15 female H 56,57757 nonsmoker
212 X82_NORM_ 15 male H 57,96578 nonsmoker
213 X57_NORM_ 15 female H 51,80276 nonsmoker
214 X35_NORM_ 16 male H 35,5729 smoker
215 X80_NORM_ 16 female H 56,37223 smoker
216 X63_NORM_ 16 female H 45,18001 nonsmoker
217 X61_NORM_ 16 female H 57,64271 nonsmoker
218 X92_NORM_ 17 female H 23,47445 smoker
219 X136_NORM_ 17 male H 59,48517 smoker
220 X89_NORM_ 17 female H 22,97057 nonsmoker
221 X138_NORM_ 17 female H 43,02247 smoker
222 X2_NORM_ 17 male H 47,92049 smoker
223 X155_NORM_ 17 female H 18,43406 nonsmoker
224 X96_NORM_ 18 female H 23,95083 smoker
225 X137_NORM_ 18 male H 52,53103 smoker
226 X104_NORM_ 18 male H 20,36676 nonsmoker
227 X148_NORM_ 18 female H 41,40452 smoker
228 X129_NORM_ 19 male H 21,76854 nonsmoker
229 X149_NORM_ 19 male H 43,3128 smoker
230 X101_NORM_ 19 male H 22,25314 smoker
231 X33_NORM_ 19 female H 50,93771 smoker
232 X109_NORM_ 19 male H 19,70694 smoker
233 X55_NORM_ 20 male H 28,94456 nonsmoker

184
Tessa_sample_workflow/rnaseqids_qc4_pass_plusref2.txt

@ -0,0 +1,184 @@ @@ -0,0 +1,184 @@
X102_NORM_
X104_NORM_
X105_NORM_
X107_210_T05_90026
X108_110_T05_90051
X108_210_T05_90062
X108_NORM_
X109_NORM_
X10_NORM_
X111_110_T02_11651
X111_NORM_
X112_110_T02_12285
X113_NORM_
X114_NORM_
X122_NORM_
X123_NORM_
X124_11_T05_90014
X124_NORM_
X125_NORM_
X128_NORM_
X129_NORM_
X130_NORM_
X13_0_T06_90295
X1320_0_T03_90210
X132_110_T06_90009
X1322_0_T04_90118
X1323_0_T04_90114
X1327_0_T05_90074
X133_210_T05_90109
X134_110_T04_90117
X135_220_T04_90135
X135_NORM_
X136_NORM_
X137_NORM_
X138_NORM_
X139_NORM_
X1401_0_T04_90183
X1402_0_T05_90007
X1406_0_T04_90217
X1408_0_T04_90132
X1410_0_T05_90120
X1415_0_T07_90003
X1417_0_T06_90320
X145_NORM_
X146_NORM_
X147_NORM_
X148_NORM_
X149_220_T04_90146
X149_NORM_
X1502_0_T05_90096
X1503_0_T06_90169
X1505_0_T07_90037
X153_NORM_
X154_110_T05_90071
X154_NORM_
X155_NORM_
X158_NORM_
X159_NORM_
X15_NORM_
X161_NORM_
X163_NORM_
X164_NORM_
X165_110_T05_90099
X166_NORM_
X16_NORM_
X172_311_T05_90061
X175_210_T06_90034
X175_311_T05_90103
X176_110_T04_90246
X17_NORM_
X18_110_T05_90100
X18_NORM_
X195_22_T04_90096
X195_311_T06_90020
X201_210_T04_90113
X201_311_T06_90280
X205_110_T04_90200
X20_NORM_
X216_110_T03_90106
X220_110_T04_90021
X22_27_T04_90144
X22_NORM_
X23_220_T05_90086
X247_110_T02_07964
X24_NORM_
X25_0_T06_90258
X25_NORM_
X28_NORM_
X2_NORM_
X304_0_T06_90224
X3_110_T05_90001
X31_NORM_
X32_NORM_
X33_0_T07_90020
X33_110_T02_12543
X33_NORM_
X353_0_T06_90035
X37_110_T06_90046
X37_NORM_
X391_0_T06_90238
X399_0_T06_90196
X39_NORM_
X40_NORM_
X413_0_T06_90159
X419_0_T06_90175
X41_NORM_
X423_0_T06_90237
X42_NORM_
X43_110_T05_90008
X433_0_T06_90135
X434_0_T06_90088
X450_0_T06_90202
X451_0_T06_90027
X45_110_T02_10969
X454_0_T06_90220
X460_0_T06_90266
X46_110_T05_90118
X464_0_T06_90221
X466_0_T06_90045
X46_NORM_
X474_0_T06_90079
X478_0_T06_90151
X47_NORM_
X487_1_T04_90142
X48_NORM_
X496_0_T06_90319
X4_NORM_
X50_110_T02_09087
X504_0_T07_90051
X51_0_T06_90222
X518_0_T06_90188
X527_0_T07_90029
X530_0_T07_90019
X53_22_T04_90131
X535_0_T07_90052
X543_0_T06_90110
X550_0_T07_90049
X55_NORM_
X57_21_T05_90106
X60_210_T06_90065
X60_NORM_
X613_0_T07_90064
X632_0_T07_90050
X63_NORM_
X641_0_T06_90063
X642_0_T07_90030
X650_0_T06_90058
X658_0_T06_90150
X66_0_T06_90281
X662_0_T06_90096
X66_NORM_
X67_0_T06_90307
X67_220_T05_90072
X68_NORM_
X695_0_T06_90053
X699_0_T06_90067
X71_NORM_
X7_21_T04_90179
X728_0_T06_90052
X730_0_T06_90064
X749_0_T06_90080
X74_NORM_
X76_110_T02_09747
X77_110_T05_90091
X77_NORM_
X78_NORM_
X80_11_T04_90157
X80_NORM_
X81_NORM_
X84_NORM_
X85_NORM_
X86_NORM_
X87_110_T06_90007
X88_NORM_
X89_NORM_
X8_NORM_
X9_0_T06_90304
X96_NORM_
X98_110_T02_10430
X98_NORM_
X99_110_T05_90056
X99_220_T05_90057
X99_NORM_
X263_110_T04_90226_2

1001
Tessa_sample_workflow/sample.htseq.txt.table

File diff suppressed because one or more lines are too long
Loading…
Cancel
Save