Hi,
Can someone please advise on the below taken from the Bowtie2 manual?
When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.
How does Bowtie2 calculate the number of characters that are trimmed or clipped from the alignment ends?
If for example, I am mapping a 100bp read to a genome by local alignment and if only 20bp's in the middle of the read align, does bowtie2 trim or clip the 40bp's from either side to maximize the alignment score?
Many thanks in advance!
Can someone please advise on the below taken from the Bowtie2 manual?
When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.
How does Bowtie2 calculate the number of characters that are trimmed or clipped from the alignment ends?
If for example, I am mapping a 100bp read to a genome by local alignment and if only 20bp's in the middle of the read align, does bowtie2 trim or clip the 40bp's from either side to maximize the alignment score?
Many thanks in advance!
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