Hi! I'm usg HTSeq v 0.6.1 to count reads mapping to features (the htseq-count script). I'm getting a
My accepted_hits.bam file is generated by mapping with STAR and then coordinate-sorted and converted to BAM using samtools.
I am using the htseq command
What is wrong and how do I fix it? (Apart from running htseq on the sam file)?
Thanks in advance,
Darya
Code:
18700000 SAM alignment record pairs processed. Error occured when processing SAM input (record #40455805 in file /scratch/me/accepted_hits.bam): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised in __init__.py:671]
I am using the htseq command
Code:
htseq-count --format=bam --order=pos --mode=union --idattr=gene_id --stranded=reverse --type=exon} $WORKDIR/accepted_hits.bam gencode.v19.gtf
Thanks in advance,
Darya
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