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



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