Hi Condomitti,

The SAM file generated by abyss-pe will only contain reads mapping to different contigs. This would be why you'll see some contigs with 0 mapped reads. 

The tool that filters the reads like this is abyss-fixmate. If you want to get all of the alignments you'll need to run abyss-map separately. 

Cheers,

Tony

On 2014-06-02, at 2:27 PM, George Willian Condomitti wrote:

Hi guys,

I assembled with SSQ=1, pe-sam mp-sam options, and then I got the .SAM output file, which gives me detailed information regarding reads on contigs mapping.

I used samtools to generate BAM file from the generated "-3.sam" file, and then indexed it and finally called "samtools idxstats", which (if I did not misunderstand) gives me the how many reads mapped to each contig.

I'm a bit confused now because some contigs have 0 as mapped reads. Shouldn't it have at least 1 read mapped back to it?

Thanks a lot.


Cheers,
Condomitti.

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