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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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HTSeq failing to count reads #91

Closed JCSzamosi closed 4 years ago

JCSzamosi commented 5 years ago

htseq-count is failing to count the overwhelming majority of my reads, despite the fact that they are almost all fully nested within features of the right type. It is returning __no_feature for more than 90% of the reads.

I don't want to upload BAM or gff files, since they are large. Should I do that? I'm not sure how to debug this.

iosonofabio commented 4 years ago

Please test the latest release and upload a small BAM file and GTF file with subsets of reads/features that focus on the problem, thank you.

I'll close in week if no activity.