Simple Bowtie question

[nilmot13]

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

[tianyub836]

try option "-m 1"

[770349688]

TMM normalization

Hello：
it is said that TMM is a normalization in RNA-seq，and I have learn it for a long time。But I don‘t understand it so far。Can you tell me how does it perform？And I would be gratefull if you could give me an example ？

[nilmot13]

try option "-m 1"

Hi,

I didn't use -m = 1 beause it will reduce the mapping coverage of some reads. E.g in the ribisomal RNA region there gene cluster are very highly conserved and our lab is still interested about its coverage.

What I was really looking for is, would the parameter I've set gave me a stringent mapping result? i.e. less mismatches and poor quality reads being mapped.

Cheers

[oxydeepu]

A simple question about bowtie output

Hi all..

i have a small doubt. In the output of bowtie, how to figure out mismatches. +ve is fine., but in negative there is reverse complementation thats what is giving me a confusion.
Please help as soon as possible.
Thank you in advance.

Deepak

[nilmot13]

Hi Deepak, what exactly are the problems that you are encounting?