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 Eric,
On 3/19/12 4:13 PM, Eric Guo wrote:
Hi there,
I have two questions regarding alignment using Bowtie:
- 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.
- 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
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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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:
- 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.
- 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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-user@lists.galaxyproject.org
-
Eric Guo -
Jennifer Jackson