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Hi there,
I was wondering if anybody knows anything about how bowtie performs alignments using a seed segment. I've been trying to use this option with some ribosome profiling data which contains reads of length 50nt. Alignment is supposed to be based on the first 21nts, which are then exteneded iteratively until you fail to align. My issue is that the bowtie changes the aligned location of the read as I increase its lengths, which from my understanding should not occur as the location should be based solely on the seed section.
For reference, an example:
The above gives locations in the latter output for some reads, not present in the former for the same read.
I was wondering if anybody knows anything about how bowtie performs alignments using a seed segment. I've been trying to use this option with some ribosome profiling data which contains reads of length 50nt. Alignment is supposed to be based on the first 21nts, which are then exteneded iteratively until you fail to align. My issue is that the bowtie changes the aligned location of the read as I increase its lengths, which from my understanding should not occur as the location should be based solely on the seed section.
For reference, an example:
Code:
bowtie -a -v 2 [ORG] -f [SEED_ONLY.fa]
Code:
bowtie -a -n 2 -l 21 [ORG] -f [FULL_READS.fa]
The above gives locations in the latter output for some reads, not present in the former for the same read.