Hello Eric, I apologize, but I made a mistake, please see below On 3/21/12 5:42 AM, Jennifer Jackson wrote:
Hi Eric,
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
On 3/19/12 4:13 PM, Eric Guo wrote: 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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