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6.8 years ago
hxlei613
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100
Hi I get FPKM for gene (not transcript) from stringtie by these parameter: -e -G -A. I also use htseq (default parameter )to generate counts matrix for the same gene sets and calculate fpkm using R. The gtf I used in this two method is the same. However the result fpkm is not the same. It seems that the overall fpkm generated by htseq is lower than stingtie. I try to use stringtie to get counts matrix for each gene but stringtie seems not generate count for gene level. I have searched the difference between them but I didn't find any answers. Thank you very much for helping me!
That is helpful. However I also find some gene whose counts are not zero in all samples and the fpkm I calculate is not zero (for example the average fpkm of such genes can be 300 or 3000) but fpkm generated by stringtie is zero. What's possible reason for that?
Without further information it's impossible for anyone to know.
Hi, do you know if StringTie computes effective feature lengths and uses those in the denominator when it computes FPKM, or if it uses the reported annotation lengths? There are so many interlocking functions in StringTie I can't extract the answer from the code without a LOT of work!