Hi,
I've been playing around with Bowtie on Galaxy platform and I would like to ask some very simple question really to confirm my understanding to the Bowtie parameters.
My aim for the mapping is to get the best sequencing alignment to a custome genome.
These are the parameter I've used:
Single-end
-n = 2
-e = 70
--nomaqround = round to nearest 10
-y
-a
--best
--maxbts = 800
--strata
Will the parameters I've set gave me a single alignment per sequence read and also ensure it's 'uniqueness/stringency'?
If anyone could help that would be fantastic.
Many thanks
I've been playing around with Bowtie on Galaxy platform and I would like to ask some very simple question really to confirm my understanding to the Bowtie parameters.
My aim for the mapping is to get the best sequencing alignment to a custome genome.
These are the parameter I've used:
Single-end
-n = 2
-e = 70
--nomaqround = round to nearest 10
-y
-a
--best
--maxbts = 800
--strata
Will the parameters I've set gave me a single alignment per sequence read and also ensure it's 'uniqueness/stringency'?
If anyone could help that would be fantastic.
Many thanks
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