Question: What's the difference of FPKM generated by htseq and stringtie?
gravatar for hxlei613
20 months ago by
hxlei61390 wrote:

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!

stringtie fpkm htseq • 983 views
ADD COMMENTlink modified 20 months ago by Devon Ryan96k • written 20 months ago by hxlei61390
gravatar for Devon Ryan
20 months ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

StringTie is able to use multimappers, which htseq will ignore them. That is the most probably cause for the difference you're seeing.

ADD COMMENTlink written 20 months ago by Devon Ryan96k

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?

ADD REPLYlink modified 20 months ago • written 20 months ago by hxlei61390

Without further information it's impossible for anyone to know.

ADD REPLYlink written 20 months ago by Devon Ryan96k
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