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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-count paired-end reads, mate wrongly assigning in 3'UTR #87

Closed uguyet closed 4 years ago

uguyet commented 5 years ago

Hello, I'm working with paired-end RNA-seq data and used HTSeq-count in order to count reads that mapped on a reference genome. I launched the command as follow: htseq-count --stranded=reverse -a 10 --order=name -t genes -i ID -m intersection-nonempty - htseq_reference_genome.gff --samout htseq_output.sam input_file.sam

Everything seem fine expect that when I check the data in IGV, I found that some reads are wrongly assigned to a gene because they mapped after the 3'UTR of this gene (no problem with the 5' UTR) and in the SAM file output, they have the gene as assignation. Just note that their mates map correctly between the start and stop of the gene.

Is there an option I forgot ?

Best regards, Ulysse

iosonofabio commented 4 years ago

Can you please send a link to the bam file or a subset thereof that shows the problem?

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