Hello
I've read the bowtie manual but am still not very clear.
I have some sRNA NGS data, and want to align using bowtie to a hairpin reference (sense and antisense sequence of a gene in one fasta file).
I would expect that a read from the hairpin would align equally well to both the sense and antisense sequence.
In this case, does bowtie randomly select the alignment to report?
Should I be aligning only to the sense or antisense sequence using the --norc or --nofw options?
Also, can anyone clarify what this means about the --best option for bowtie:
"--best mode also removes all strand bias"
Thanks for any advice!
kennels
I've read the bowtie manual but am still not very clear.
I have some sRNA NGS data, and want to align using bowtie to a hairpin reference (sense and antisense sequence of a gene in one fasta file).
I would expect that a read from the hairpin would align equally well to both the sense and antisense sequence.
In this case, does bowtie randomly select the alignment to report?
Should I be aligning only to the sense or antisense sequence using the --norc or --nofw options?
Also, can anyone clarify what this means about the --best option for bowtie:
"--best mode also removes all strand bias"
Thanks for any advice!
kennels
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