feature counts vs readspergene.out.tab for DESeq2 count matrix

Hello! I have readspergene.out.tab as an output after running star. Is it possible to create a count matrix using that file for input into DESeq2 using galaxy, instead of running feature count as per the galaxy DESeq2 tutorial?

Welcome, @kayleen !
Sorry I think I don’t understand your question. You want to use “readspergene.out.tab > DESeq2” instead of “BAM (mapped reads)+GTF>HTseqcount>DESeq2” ?

Star manual, about the per genes option, states that:

7 Counting number of reads per gene.
With --quantMode GeneCounts option STAR will count number reads per gene while mapping. A read is counted if it overlaps (1nt or more) one and only one gene. Both ends of the paired-end read are checked for overlaps. The counts coincide with those produced by htseq-count with default parameters. This option requires annotations in GTF format (i.e. gene id tag for each exon) specified in --sjdbGTFfile at the genome generation step or at the mapping step provided in option. STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options:(…)

So I guess you are good to go.

If you’re asking about the DESeq2 input structure, you can check the DESeq2 manual and see some example input data

Hi David,

Thank you for your reply! I managed to convert my read counts per gene by extracting the second column :slight_smile: If that helps anyone else facing the same problem as I did!


Nice. Thanks for sharing :+1:

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