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Question: Aligning Long Reads
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gravatar for Shalabh Sharma
7.2 years ago by
Shalabh Sharma • 20
Shalabh Sharma • 20 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
bwa alignment • 1.0k views
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modified 7.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.2 years ago by Shalabh Sharma • 20
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gravatar for Jennifer Hillman Jackson
7.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.2 years ago by Jennifer Hillman Jackson ♦ 25k
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
ADD REPLY • link written 7.2 years ago by Bob Harris • 190
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