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
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
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