Bwa, Aln Or Index
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12.8 years ago
Liyf ▴ 300

Hi! This is my first time to analysis exome sequencing data. First I should do the mapping. I choose BWA. BWA has two different algorithms: index command and aln commands, any suggestions about how to choose, and the parameter? Thanks.

bwa index • 4.1k views
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12.8 years ago
toni ★ 2.2k

Just to get you on track :

1 - you have first to index the genome reference (human or other...) : bwa index

2 - then only you will be able to map back your reads to the genome. : bwa aln

3 - Finally depending on your experiment type (single end or paired end) : bwa samse or bwa sampe

For detailed algorithm explanation and parameters specifications, have a look to the link given by Istvan.

Cheers, Tony

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Index has two selections: Is and bwtsw, I think they just differ in the size of database, am I right? Thanks for you getting me on track!

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I got it, thanks.

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But I still have a little confused, the outfile of bwa index does not use in the next step, is it useful? In addition, index have two selection, any difference?

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Yes you are right. For instance you cannot use 'is' method for whole human genome.

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12.8 years ago

Please read the manual first. You will see that it contains the answer to just about all of your present and future questions.

http://bio-bwa.sourceforge.net/bwa.shtml

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