Hello All,
I like to apply HTSeq-count on a .bam file, but if I directly pipe the output of samtools to htseq it gives me an error. However, if I first write the sorted file in a temporary file and then apply samtools-view and htseq-count on this temp file, there is no error!
Do you know what might be causing this problem?
Case (1): [generates error]
$ samtools sort -on -m 300000000 accepted_hits.bam | samtools view -h - | htseq-count -m union - hg19.gtf > output.count
Error occured when reading first line of sam file.
[Exception type: StopIteration, raised in count.py:83]
Case (2): [no error!]
$ samtools sort -n -m 300000000 accepted_hits.bam temp-sorted.bam
$ samtools view -h temp-sorted.bam | htseq-count -m union - hg19.gtf > output.count
Thank You,
NF
I like to apply HTSeq-count on a .bam file, but if I directly pipe the output of samtools to htseq it gives me an error. However, if I first write the sorted file in a temporary file and then apply samtools-view and htseq-count on this temp file, there is no error!
Do you know what might be causing this problem?
Case (1): [generates error]
$ samtools sort -on -m 300000000 accepted_hits.bam | samtools view -h - | htseq-count -m union - hg19.gtf > output.count
Error occured when reading first line of sam file.
[Exception type: StopIteration, raised in count.py:83]
Case (2): [no error!]
$ samtools sort -n -m 300000000 accepted_hits.bam temp-sorted.bam
$ samtools view -h temp-sorted.bam | htseq-count -m union - hg19.gtf > output.count
Thank You,
NF
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