Bowtie Seed length (-l) and non-unique reads mode (m=-1)
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? 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
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
Hi Eric, 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. 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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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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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participants (2)
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Eric Guo -
Jennifer Jackson