naive question, but do not find a clear answer to solve this,
downloaded a raw count file from geo, which looks like this,
gene unstranded fwd rev
ENSMUSG00000102693 0 0 0
ENSMUSG00000064842 0 0 0
ENSMUSG00000051951 63 38 25
How could I use this file to generate the count table? or I can just simply use the count of the unstranded?
Thanks
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written
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leisureh •
In theory you should first check the metadata of that experiment and check if they had stranded or un-stranded data .
If that is not available for whatever reason, I would personally go with the unstranded data indeed (which was the common mode before we switched to doing stranded seq by default) .
If you want to go for the stranded one, you will have to look up the strand of each gene and take the count that is reported for that strand.
You want to look at more rows of data to be sure (obviously the genes with 0 counts tell you nothing), but that pattern of the left, unstranded column having about as many reads as the forward and reverse columns together suggests that your data is unstranded, so that is the correct column to use. If your data were stranded, the unstranded count would be just about what either the forward or reverse columns would be, and the other direction would be mostly empty. (Like 63,0,63 or 63,63,0)
just to add to the confusion, if the data were paired-end, then the two counts would also be very close regardless of whether the sequencing was stranded or not
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