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
