First of all,
hello to everyone, I am beginning to do RNAseq analysis in bacteria and this forum has been of immense help so far, unfortunately I have not seen anyone with this issue yet:
My system: Windows 7, running BioLinux 7 in Virtual Machine.
Python 2.7.3
HTSeq 0.5.4p3
Numpy 1.6.1
I was trying to count my mapped reads using a pipe with samtools:
samtools view -h sorted.bam | htseq-count -m intersection-nonempty - reference.gff
The error I got was:
4410 GFF lines processed.
Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in count.py:199]
Not sure where to go from here, it feels like I may be missing a module or something.
Any and all help is appreciated!
hello to everyone, I am beginning to do RNAseq analysis in bacteria and this forum has been of immense help so far, unfortunately I have not seen anyone with this issue yet:
My system: Windows 7, running BioLinux 7 in Virtual Machine.
Python 2.7.3
HTSeq 0.5.4p3
Numpy 1.6.1
I was trying to count my mapped reads using a pipe with samtools:
samtools view -h sorted.bam | htseq-count -m intersection-nonempty - reference.gff
The error I got was:
4410 GFF lines processed.
Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in count.py:199]
Not sure where to go from here, it feels like I may be missing a module or something.
Any and all help is appreciated!
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