Hi,
anyone know how to solve these cigar type errors in HTseq? Seems ti is unusable until its solved..
python -m HTSeq.scripts.count in_sorted.bam ref.gff -f bam -s no -t CDS -m union -i locus_tag
Error occured when reading beginning of SAM/BAM file.
Unknown CIGAR code '=' encountered.
[Exception type: ValueError, raised in _HTSeq.pyx:1163]
Or better yet, another progam to get raw counts from bam and gff files. Don't say 'bedtools' because that doesn't work either.. endlessly gives '0' as all the counts.
Thanks,
S.
anyone know how to solve these cigar type errors in HTseq? Seems ti is unusable until its solved..
python -m HTSeq.scripts.count in_sorted.bam ref.gff -f bam -s no -t CDS -m union -i locus_tag
Error occured when reading beginning of SAM/BAM file.
Unknown CIGAR code '=' encountered.
[Exception type: ValueError, raised in _HTSeq.pyx:1163]
Or better yet, another progam to get raw counts from bam and gff files. Don't say 'bedtools' because that doesn't work either.. endlessly gives '0' as all the counts.
Thanks,
S.
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