What's the difference of FPKM generated by htseq and stringtie?
1
0
Entering edit mode
2.9 years ago
hxlei613 ▴ 90

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!

fpkm stringtie htseq • 1.4k views
ADD COMMENT
2
Entering edit mode
2.9 years ago

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

ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2450 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6