Shalabh,
Not to toot my own horn, but I believe lastz should do a better job
than bwa for reads longer than about 100 bp. bwa will run faster, but
my understanding is that it will not find many reads with more than 3
mismatches. Moreover, if your reads are from 454, which is subject to
short indel sequencing errors, I believe reads with these errors will
generally be missed by bwa.
I good test on your data would be to take a random sample of 10,000
reads and try mapping them with both tools, and see which one gives
you more believable results.
You could also post your question to seqanswers.com-- describe your
data (dna or rna, read lengths, sequencing technology, expected
divergence between your sample and the reference, how you prefer non-
uniquely aligning reads to be handled, etc.) and ask for advice about
the pros and cons of different aligners/mappings.
Bob H
On Oct 4, 2011, at 8:21 PM, Jennifer Jackson wrote:
Hello Shalabh,
BWA is a good choice for longer reads, if they are DNA. If you have
RNA data, then you might want to consider a tool like BLAT or BLAST
(is wrapped for Galaxy in the Tool Shed).
To use BLAST in Galaxy, you will need a local or cloud instance, as
explained here:
http://getgalaxy.org
http://galaxyproject.org/wiki/Tool%20Shed
Hopefully this helps,
Jen
Galaxy team
On 10/3/11 7:50 AM, Shalabh Sharma wrote:
Hi,
I am new to mapping.
I have reads ranging from 150-300bp, i am not sure which is the best
suitable program for that in Galaxy.
I already tried bwa but i am not sure if thats the best choice for
long
reads.
Thanks
Shalabh
___
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:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___
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:
http://lists.bx.psu.edu/
___
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:
http://lists.bx.psu.edu/
