Hi guys,
I previously run Bowtie on short read sequences in raw format (i.e. one sequence per lane with no other lines in the file). I want to compare the alignment by Bowtie to BWA. I looked through BWA manual (http://bio-bwa.sourceforge.net/bwa.shtml) and it seems to me that only fastq input format is acceptable. Is it so? And if it is so, can I make a fake fastq with mock ID and quality lines and expect BWA to work appropriately?
Also, I am not sure if I should use 'bwa aln' or 'bwa samse'. I want to produce SAM in the end, so it seems that I need to use samse. However I don't see how I can control any of the parameters with samse. I would like to discard alignments that map to more than one place in the genome, not to allow any gaps, at most allow one mismatch and run the program on 4 cores and produce SAM. It's really easy with Bowtie, but is it something that I can do with BWA?
thanks
I previously run Bowtie on short read sequences in raw format (i.e. one sequence per lane with no other lines in the file). I want to compare the alignment by Bowtie to BWA. I looked through BWA manual (http://bio-bwa.sourceforge.net/bwa.shtml) and it seems to me that only fastq input format is acceptable. Is it so? And if it is so, can I make a fake fastq with mock ID and quality lines and expect BWA to work appropriately?
Also, I am not sure if I should use 'bwa aln' or 'bwa samse'. I want to produce SAM in the end, so it seems that I need to use samse. However I don't see how I can control any of the parameters with samse. I would like to discard alignments that map to more than one place in the genome, not to allow any gaps, at most allow one mismatch and run the program on 4 cores and produce SAM. It's really easy with Bowtie, but is it something that I can do with BWA?
thanks
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