Geo Pertea

The *.tracking file is not supposed to show all the reference transcripts, its purpose is to _track_ assembled transcripts across samples (i.e. transcripts from A.gtf and B.gtf in your case)....

It looks like it is a problem in the (old) GFF parsing code used there which stumbles trying to understand some of the recent transcript definitions.. I am going to...

Just pushed the update in the develop branch. However that is NOT a stable branch for production use so I also prepared a source update tarball for the old official...

OK, statically linked Linux build here: http://ccb.jhu.edu/dl/cufflinks-2.2.1-gffpatch.Linux_x86_64.tar.gz Haven't gotten around to test it on your full GRCm38.86 example, getting those files and building the hisat2 index takes a while --...

I've just finished running your _example_workflow_gff3.sh_ and it was successful with the patched binaries. I'll run the GTF version next (just from the cufflinks commands of course), to make sure...

It looks like it's the new "Selenocyteine" feature lines added by Ensembl which are now confusing the parser -- I would suggest using something like `grep -vP '\tSelenocysteine\t'` to remove...

yes, that would work. You can use the compressed file directly (that's what I did): ``` zcat Mus_musculus.GRCm38.86.gtf.gz | grep -vP '\tSelenocysteine\t' > GRCm38.86.bye_seleno.gtf ```

Thank you for reporting this, I will look into a possible fix for what looks like a mishandling of soft-clipping.This probably happens because Cufflinks was designed (and tested) to work...

Yes, this patch should be OK for _testing_, I am quite confident it is a likely fix for the soft-clipping problem reported here. I'm just hoping it doesn't introduce _other_...

Is there such coverage data in the given GTF: `stringtie_merged.gtf` ? gffcompare does not compute coverage, it only fetches the existing coverage values from the input GTF, which are going...