Multiple columns in RNAseq count matrix?

Question

[Jeff-Gui]

Hi, in GSE131592, each file corresponds to the counting matrix of one sample. In each file there are three columns. Does anyone know how to get the count of this sample?

The picture shows GSM3790428 as an example. No reply from the dataset author yet.

Answer 1

[swbarnes2]

That is htseq count data. The three columns represent the number of reads assigned to that gene assuming the library is 1) unstranded 2) stranded in the forward direction, 3) stranded in the reverse direction.

[Jeff-Gui]

Thanks. Without checking raw reads to see how exactly the library is generated, is it reasonable to simply take the second column because of the much fewer ambiguous count than the first?

[swbarnes2]

I'd look over more of the columns, and if the general trend is that columns 1 and 2 are nearly the same, that means the prep is stranded forward, and you should use column 2.