Question: What's the difference of FPKM generated by htseq and stringtie?
0
gravatar for hxlei613
8 months ago by
hxlei61380
Bangladesh
hxlei61380 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 • 515 views
ADD COMMENTlink modified 8 months ago by Devon Ryan91k • written 8 months ago by hxlei61380
2
gravatar for Devon Ryan
8 months ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k 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 8 months ago by Devon Ryan91k

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 8 months ago • written 8 months ago by hxlei61380

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

ADD REPLYlink written 8 months ago by Devon Ryan91k
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