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:
Commands:
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.
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.
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