stringtie does not show results of all genes
0
0
Entering edit mode
6 months ago
bart ▴ 20

Hi,

I'm using stringtie for transcript assembly in galaxy with the output gene abundance estimation file turned on so TPM and FPKM counts are also outputted. What's strange to me is that in the gene abundance estimation file of some samples there are more outputted lines than in others. This means that for an unknown reason the results of some genes are outputted in one sample but not in the other. Is this normal and why does this happen?

stringtie galaxy • 287 views
ADD COMMENT
0
Entering edit mode

I just found this answer by @Kevin Blighe (Stringtie output files):

"The one that was not included has coverage that falls below the threshold. It is virtually not expressed at all. Modify the -C and -c parameter to StringTie: -C <cov_refs.gtf> StringTie outputs a file with the given name with all transcripts in the provided reference file that are fully covered by reads (requires -G). -c <float> Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2.5"

Now my question would be: can I just fill in 0 for the FPKMs and TPMs of all the genes that are not included? I'm trying to use the outputted file for differential expression analysis

ADD REPLY

Login before adding your answer.

Traffic: 1529 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