Thread: BWA index
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Old 01-22-2010, 01:05 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default BWA index

Dear group,

Previously I used index like the following on human genome:

bwa index -a bwtsw -c Hsapiens37.fasta

I ran the subsequent analysis steps and compared the end result with others where they just used

bwa index Hsapiens37.fasta
and carried out end analysis resulting in .sam file.

now when i compare results from -a bwtsw option to no parameter indexing (2nd option), majority of reads are aligned reversed etc.

one should use this option or not?
what happns using -a bwtsw and -c and what happens if I dont.

could some one help me here. thanks
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