Hi Simon,

It appears that one of my regular unsorted SAM files is truncated.

Though the sort works fine and samtools view does not detect truncation
in my file.sam.bam, I still get error messages after attempting to generate
counts files.

samtools view -h file.sam.bam | python dexseq_count.py file.gff -
file.counts

Do you think that the truncation may be behind the problems?

I can't check the structure of my SAM.BAM file because its all symbols,
though when I use samtools view, the contents runs across the screen, and I
am unable to pinpoint any irregularity.

Thanks,
Margaret

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