Question: Stringtie Deseq2/EdgeR count tables all zero
0
gravatar for scholtz
6 days ago by
scholtz60
Hungary
scholtz60 wrote:

Dear Galaxy Team,

I encountered a different problem with Stringtie + output additional files for DESeq2/EdgeR. Running the external GTF dataset (hg19 reference) through Stringtie Merge indeed makes it acceptable for Stringtie + output...etc., but the count tables are are all zero for every transcript or gene. IGV shows very clearly the reads in the bam files and the transcript assembly was also succesful. If I used the Assembled transcripts.gtf from Stringtie itself in a second round of Stringtie + output...etc., I got counts in the transcript and gene count tables. If I ran the same Assembled transcripts.gtf through Stringtie Merge as the input_gtf, and used the "merged" gtf for a second round of Stringtie + output...etc., again I got zero counts in the transcript and gene count tables. I also tried merging the external gtf and the Assembled transcripts.gtf from Stringtie, but using that also resulted in zero counts. Am I missing something? Your help would be appreciated,

Beata

ADD COMMENTlink modified 6 days ago by Jennifer Hillman Jackson23k • written 6 days ago by scholtz60
0
gravatar for Jennifer Hillman Jackson
6 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi Beata,

A common problem encountered that results in poor or unexpected counts is when the reference genome and reference annotation have a chromosome identifier mismatch. Sorting can also sometimes be a factor as can the settings used during alignment.

Help to troubleshoot can be found in these places:

If working at https://usegalaxy.org or the problem can be reproduced there, and you cannot determine the root issue and fix it, a bug report can be sent in for direct feedback based on your exact data.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 days ago • written 6 days ago by Jennifer Hillman Jackson23k
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