Tag Archives: SAM

bowtie and multimapping reads

Posted on November 26, 2011 by Davo

I first tried this with BWA. Now I’ll try it with bowtie. Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: … Continue reading →

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bwa and multi mapping reads

Posted on October 11, 2011 by Davo

Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: >tag ACGTACGTACGTACGTAGGTACGTA Using bwa (Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.9-r1) this is the SAM output tag 0 artificial 57 0 25M * 0 0 ACGTACGTACGTACGTAGGTACGTA … Continue reading →

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Mapping qualities

Posted on September 14, 2011 by Davo

Short read alignment programs, such as bwa, usually have a mapping quality score for each read that is aligned to a reference. I came across this useful post in seqanswers and here I try to replicate it with an example … Continue reading →

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Perl and SAM

Posted on January 28, 2011 by Davo

Lincoln Stein has written a bunch of modules to deal with SAM/BAM files. Check out the CPAN module. To install the Perl module on a machine where you don’t have root access, follow these instructions. Using this module, I recreated … Continue reading →

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