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Old 10-17-2014, 03:20 AM   #9
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Location: Toulouse, France

Join Date: Oct 2014
Posts: 5

Originally Posted by WhatsOEver View Post
2) Your "GC01.concordant_uniq" file is a sam file created from one of the bam files using samtools view -h file.sam > GC01.concordant_uniq, isn't it? A more accurate comparison would be to use "diff file1 file2". If the output is empty, your files are equal.
No, my sam files are gsnap output, not made with samtools view, then I'm trying to have bam files...

I'm currently trying an other thing : error could maybe be linked with different names between my fasta file and inside my fasta file, in the header. I homogenize everything, and if it doesn't change anything, I'll ask for an update of samtools version to the bioinformatics server I use...

Thanks again !
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