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.
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
Please read the manual first. You will see that it contains the answer to just about all of your present and future questions.
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version 2.3.6
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!
I got it, thanks.
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?
Yes you are right. For instance you cannot use 'is' method for whole human genome.