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Magdoll / Cogent

Coding Genome Reconstruction using Iso-Seq data
BSD 3-Clause Clear License
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Sanity check failed by "filter_away_subset.py" #100

Open unique379r opened 2 years ago

unique379r commented 2 years ago

Hi All steps before "Filter away 5' degraded isoforms" were good, NO Error was reported but this script generates NO OUTPUT but just these stdout:

filter_away_subset.py testSample.collapsed

The number of PBID records in the files disagree! Sanity check failed.
# of PBIDs in testSample.collapsed.rep.fq: 660
# of PBIDs in testSample.collapsed.gff: 660
# of PBIDs in testSample.collapsed.abundance.txt: 658

I was suspecting that it might be because i used "--dun-merge-5-shorter" option in collapse_isoforms_by_sam.py but thats not the case.

Note:

  1. I had used uLTRA aligment on HQ reads generated by isoseq3.
  2. fusion_finder.py does not support BAM file just SAM, can you update it as collapse_isoforms_by_sam.py does supports BAM with -b.

Please help!

Thanks Rupesh Kesharwani