BWA samse help for a new user

[calatian]

Hello,

I am a new user of BWA and Bioinformatics in general. I am having some problems running BWA samse and am hoping somebody could give me some general idea of what I am doing wrong.

I have the Ecoli genome in .fa format and am generating reads (the last try was with 10000 reads of 100bp each) in .fq format.

I am working on a school project and need to evaluate BWA Backtrack's performance on these reads in order to try to improve it afterwards with the seed-chain-extend technique.

These are the files I have, and the commands I am running:

• Ecoli.fa (the genome)
• reads.fq (the 10000 reads I generated)

Commands:

• bwa index ecoli.fa (which generates ecoli.fa.amb, ecoli.fa.ann, ecoli.fa.bwt, ecoli.fa.pac, ecoli.fa.sa)
• bwa aln ecoli.fa reads.fq > out.sai (which seems to work fine and generates out.sai)
• bwa samse ecoli.fa out.sai reads.fq > out.sam

As soon as I enter the last command, BWA crashes and generates an empty out.sam file.

As I mentioned, I am very new to the program and would appreciate any details regarding what I am doing wrong and point me in the right direction.

Also, I would really appreciate if I could get information (correct commands) on how to use the above files and BWA samse for paired-end mapping, since I have not been able to make it work so far. Thank you very much.

[dpryan]

Your commands appear correct. Try running bwa in a debugger to find out what's going wrong.

[calatian]

Your commands appear correct. Try running bwa in a debugger to find out what's going wrong.

Thank you for confirming; I though the problem was with my commands so your comment was a big change in direction. After a couple of days trying to debug, I just had to install a completely different version of BWA and that worked. If somebody has a similar problem, I would simply recommend doing the same. Thanks again!