convert STAR ReadsPerGene.out.tab to Deseq2 count table

Question

[jonessara770]

Hello,

How can I format STAR ReadsPerGene.out.tab for stranded RNA to Deseq2 count matrix format?

N_unmapped 663817 663817 663817

N_multimapping 1232697 1232697 1232697

N_noFeature 5408215 8176752 5438049

N_ambiguous 108068 315 106321

NM_214429 0 0 0

NM_214220 0 0 0

NM_001143697 51 0 51

NM_001164649 1 0 1

NM_001044603 2 0 2

NM_001244242 479 1 478

NM_001244241 286 1 285

NM_001177907 428 0 428

thanks

Answer 1

[h.mon]

I use the following code snippet:

ff <- list.files( path = "./counts", pattern = "*ReadsPerGene.out.tab$", full.names = TRUE )
counts.files <- lapply( ff, read.table, skip = 4 )
counts <- as.data.frame( sapply( counts.files, function(x) x[ , number ] ) )
ff <- gsub( "[.]ReadsPerGene[.]out[.]tab", "", ff )
ff <- gsub( "[.]/counts/", "", ff )
colnames(counts) <- ff
row.names(counts) <- counts.files[[1]]$V1

Depending on the strandedness of you library, number may be 2,3 or 4.

[Kayleen]

Hello! Sorry for bringing up this old thread, but I have been trying to convert my readspergene file to a count matrix for DESeq2 as well.

Everything works fine for me, until the colnames(counts) <- ff I face this error: Error in names(x) <- value : 'names' attribute [27] must be the same length as the vector [0]

I assume this is because I have missing values in my dataset, however everything looks fine after briefly looking through my ReadsPerGene.out.tab. Could I enquire if anyone has came across this error as well and what can I do to solve it? Thank you!