Geo Pertea

Indeed this hasn't been fixed even in the current version, but it definitely should be addressed. I'll take a look at this soon.

Extending this all the way to distant and inter-chromosomal trans-splicing would break the locality assumptions (the "locus" concept). Clustering transcripts into loci would become messy without splitting these distantly trans-spliced...

It's stuck because it's waiting for input at stdin (sorry, that was meant to make it easy to use in a shell command chain with pipes etc.) Use `gffread -h`...

Unfortunately those spliced alignments which lack the XS tag are currently just discarded (skipped over) by StringTie, so they will not contribute to the assembly and abundance estimation at all.....

I didn't quite mean that, the lack of the XS tag could still be a problem - as I mentioned, spliced alignments are ignored if they lack the XS tag,...

Yes, that understanding of the effect of the missing XS tag is correct -- only single-exon alignments are then seen by StringTie, so the output will consist only of single-exon...

That bundle does seem quite large and junction rich, though Stringtie should be able to handle it in 64GB I think.. Anyway, I'm now quite curious to see what's going...

thank you, got the files and was able to reproduce the problem (it crashes the same even on Linux). Noticed that assembling the two bundles separately works fine, only assembling...

Yes, see the protocol outlined at https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#de Yes, `stringtie --merge` takes as input the .gtf files which are the output of the assembly of individual sample (`.bam`) files. Alternatively, one...

OK, I checked this manually (somehow I thought you checked it yourself before posting this) and it looks like the protein translation gffread provides is the correct translation of the...