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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-- 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:
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