bwasw

[Bgansw]

Hello,

I'm new to bioinformatics, and need help with bwasw.

I'm trying to align my sample illumina bacterial genome to an already published reference bacterial genome. The aim is to find out what genes are present in my sample genome, but missing in the reference. The plan of action was to run bwasw, and then pull out the sequence in the sample genome that do not align to the reference, then look at what these sequences are.

So far, I've run the following successfully:

bwa index -a bwtsw database.fasta

bwa bwasw database.fasta long_read.fastq > aln.sam

I've gotten a .sam output file, the size of which is 796M.

What should I do next?

Please help!

bgansw

[GenoMax]

You will want to convert the SAM files to BAM using "samtools".

You can then recover the reads that do not align to the reference genome using the directions in post #6 in this thread: http://seqanswers.com/forums/showthread.php?t=16743

[Bgansw]

Thank you Genomax.

I've been able to successfully extract the mapped and unmapped reads, thanks to your advice. I did have a query though, and I've posted it along the thread you'd specified in your post.

Thank you very very much. I'm very grateful for your help.

Regards

bgansw