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Old 08-08-2012, 12:24 AM   #10
Location: Leiden

Join Date: Jun 2009
Posts: 10


Thanks for your quick reply. If my current run with 2.08 fails I'll try 2.07

In the meantime I looked at the bowtie2 manual and found this mode:

-a mode: search for and report all alignments

-a mode is similar to -k mode except that there is no upper limit on the number of alignments Bowtie 2 should report. Alignments are reported in descending order by alignment score. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. See the SAM specification for details.

Some tools are designed with this reporting mode in mind. Bowtie 2 is not! For very large genomes, this mode is very slow.

Is this of any use to you?


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