HTSeq-count issue

[zuco]

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!

[dpryan]

I've had that happen on truncated BAM files before. Have a look at the GFF file after line 4410 (or maybe at the beginning of the BAM file, if that's near the end of your GFF) to see if something is amiss.

[zuco]

Hi,

I've had that happen on truncated BAM files before.

you were spot on. Turns out the unmapped reads were the issue, I fixed it by changing my pipe so that the samtools command included -F 4:

samtools view -h -F 4 sorted.bam | htseq-count -m intersection-nonempty - reference.gff

Thank you!