Bowtie Seed length (-l) and non-unique reads mode (m=-1)

[ericguo]

Hello all,

I have two questions regarding alignment using Bowtie:

1. Is there a way to set the Seed Length (-l) to the full length of each read instead of using a single Seed Length for all reads?

2. When using m = -1 mode ("Suppress all alignments for a read if more than n reportable alignments exist (-m): OFF"), will a read be randomly assigned to one of the alignment positions in the genome? Or, will all the alignments for one single read be reported in the final output .bam file.

Thanks in advance for your help.

-Eric

[arvid]

1. You can switch from the default "-n" alignment mode to the "-v" alignment mode to achieve this. Details: http://bowtie-bio.sourceforge.net/ma...alignment-mode

2. You mean "-m 1", not "m= -1". No alignments will be reported if more than one possible alignment according to the specified alignment criteria are found, when using this option (http://bowtie-bio.sourceforge.net/ma...wtie-options-m). If you want random assignment, use -M instead (http://bowtie-bio.sourceforge.net/ma...wtie-options-M).

[ericguo]

Hi arvid,

Thanks a lot for your reply.

-Eric