Slightly different use case to no avail!

[rebeelouise]

Hello!

Great tool, thank you!

I have completed some Nano3P'Seq, and now trying this tool to pick out some information.

I have had to convert a GFF3 file to GTF (I used gffread), and the alignment step is printing out empty files :(.

src/get_transcript_ends.py --firststrand -q0 -o transcript_ends.tsv.gz -a genome.gtf -b algs.bam [algs2.bam ... algsN.bam]

I had to remove the end in square brackets to get this to run - is this correct or does it need to be there? I have ofc changed the fasta and gtf to my references in the command I have used!

Would your suspicion be that it's poor conversion to GTF?

I know that my target is there from some basic analysis and plotting. So it's just about getting this part right.

Another thing, for different barcodes, I need to map to different references, is there a way to split this?

Really keen to get this working, so any advice appreciated!

[rebeelouise]

Okay seems to have ran just with the GFF3 file :) good to know!!

[rebeelouise]

isoquant.py - can't find this script on the repo!

[rebeelouise]

isoquant.py - can't find this script on the repo!

okay - need to call to path in conda/envs folder!

[rebeelouise]

Hello again polyTailor team. I'm running into some issues with the isoquant step, and that's because my use case is not for eukaryotic RNA.

I've raised an issue with them here: ablab/IsoQuant#263 (comment)

I would be really keen to chat about this application with you to see where I could make sensible adaptations on your workflow? Please do let me know if you're interested!

Best,

Rebee