Hello Eric,

I apologize, but I made a mistake, please see below

On 3/21/12 5:42 AM, Jennifer Jackson wrote:
Hi Eric,

On 3/19/12 4:13 PM, Eric Guo wrote:
Hi there,

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?
The seed length is a single input value for all sequences in any
particular job.


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.
If alignment are not suppressed, then all reportable hits are in the
output.

This is incorrect. If alignments are not suppressed, then reporting "-a" (all) is not the default. Rather, there are several 'reporting options', and they are used in combination and with 'alignment options' to achieve different output results. It is probably best to show you the documentation, so that you can compare different parameters and output they produce. Please see:

http://bowtie-bio.sourceforge.net/manual.shtml#reporting


Hopefully this clears up any confusion my original reply may have caused!

Jen
Galaxy team


More about Bowtie can be found here:
http://bowtie-bio.sourceforge.net/index.shtml

Best,

Jen
Galaxy team

Thanks in advance for your help.

-Eric


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