Question

Create count matrix from multible quant sf files from different directories

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JG13 • 0

@eeb93914

Last seen 4 months ago

Greece

Hi, i have multiple quant.sf files in different directories with names SRX1022857, SRX1022858, SRX1022859 etc

files <- list.files(pattern = "SRX")
> files
 [1] "SRX1022857" "SRX1022858" "SRX1022859" "SRX1022860" "SRX1022861" "SRX1022862" "SRX1022863" "SRX1022864" "SRX1022865" "SRX1022866" "SRX1022867"
[12] "SRX1022868" "SRX1022869" "SRX1022870" "SRX1022871" "SRX1022872" "SRX1022873" "SRX1022874" "SRX1022875" "SRX1022876" "SRX1022877" "SRX1022878"
[23] "SRX1022879" "SRX1022880" "SRX1022881" "SRX1022882" "SRX1022883" "SRX1022884" "SRX1022885" "SRX1022886" "SRX1022887" "SRX1022888" "SRX1022889"
[34] "SRX1022890" "SRX1022891" "SRX1022892" "SRX1022893" "SRX1022894" "SRX1022895" "SRX1022896" "SRX1022897" "SRX1022898" "SRX1022899" "SRX1022900"
[45] "SRX1022901" "SRX1022902" "SRX1022903" "SRX1022904" "SRX1022905" "SRX1022906" "SRX1022907" "SRX1022908" "SRX1022909" "SRX1022910" "SRX1022911"
[56] "SRX1022912" "SRX1022913" "SRX1022914" "SRX1022915" "SRX1022916" "SRX1022917" "SRX1022918" "SRX1022919" "SRX1022920" "SRX1022921" "SRX1022922"
[67] "SRX1022923" "SRX1022924" "SRX1022925" "SRX1022926" "SRX1022927" "SRX1022928" "SRX1022929"

How can I use library(tximport) to create a count matrix for all of them?

tximportData tximport salmon • 567 views

ADD COMMENT • link 5 months ago JG13 • 0

score 0 · Answer 1 · 2024-06-03

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Michael Love 42k

@mikelove

Last seen 20 hours ago

United States

With Bioconductor software, start by checking out the vignette first. You can find this either on the website or from within your R session:

Go to package landing page, then go down to "Documentation" and look for an HTML vignette (for my software I have HTML output)
Run the command browseVignettes("package-name")

ADD COMMENT • link 5 months ago Michael Love 42k

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each SRX* is a directory and inside this directory there is a quant.sf file with the same name. I am confused how to use the files in order to import the names for each sample and the number of reads with tximport to create a count matrix. In previous case I used quant.sf but from the same directory like that

files <- list.files(pattern = "\\.sf$")
names(files) <- paste0("quant", 19:24)
all(file.exists(files))

But I am wondering how to import them if I am in a directory called salmon and inside this there are all SRX1022857.... folders I do

library(tximportData)
dir <- system.file("salmon_res", package="tximportData")
list.files(dir)

But it doesn't list anything although that inside salmon_res there are all directories with SRX10*

ADD REPLY • link 5 months ago JG13 • 0

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fls <- dir("^SRX[0-9]+$", "quant.sf", full.names = TRUE)

Edited to add a missing quote

ADD REPLY • link 5 months ago James W. MacDonald 67k

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i tried it but this also returns character(0).But I managed to do it in a different way I specify the dir manually , list the files , provide a csv with the names of each directory and specify the files and then use the tximport

dir2 <- "/Desktop/_pipeline"
list.files(dir2)
samples <- read.table(file.path(dir2, "sampleshee.csv"), sep=",", header = TRUE)
samples
samples$sampleID
files <- file.path(dir2, "salmon_res", samples$sampleID, "quant.sf")
all(file.exists(files))
txi.inf.rep <- tximport(files, type = "salmon", txOut = TRUE)

ADD REPLY • link 5 months ago JG13 • 0