Question for the Bowtie experts out there:
If I was to generate a bowtie index from a single chromosome, rather than the full genome, and align my reads to this "chromosome-index", would you expect any sort of bias/error in the alignment results? This would be for 42 bp, single end reads from size-selected genomic DNA.
I expect that if Bowtie's options are set to only align unique reads with no mismatches, there shouldn't be a difference between whole-genome and single chromosome index alignments. However, if mismatches were allowed, I would expect that more reads would align to the single chromosome index. Does this sound correct?
I will test it out and post my findings, but if someone already knows the answer, I'd really appreciate hearing more about it.
Thanks in advance,
jjw
If I was to generate a bowtie index from a single chromosome, rather than the full genome, and align my reads to this "chromosome-index", would you expect any sort of bias/error in the alignment results? This would be for 42 bp, single end reads from size-selected genomic DNA.
I expect that if Bowtie's options are set to only align unique reads with no mismatches, there shouldn't be a difference between whole-genome and single chromosome index alignments. However, if mismatches were allowed, I would expect that more reads would align to the single chromosome index. Does this sound correct?
I will test it out and post my findings, but if someone already knows the answer, I'd really appreciate hearing more about it.
Thanks in advance,
jjw
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