Simple Bowtie question

nilmot13 · 02-07-2012, 08:26 AM

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 · 02-07-2012, 04:54 PM

try option "-m 1"

770349688 · 02-07-2012, 05:04 PM

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 · 02-08-2012, 01:19 AM

Quote:

Originally Posted by tianyub836

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 · 03-07-2012, 01:56 AM

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 · 03-07-2012, 02:03 AM

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

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02-07-2012, 08:26 AM	#1
nilmot13 Member Location: Leeds, UK Join Date: Jan 2011 Posts: 19	Simple Bowtie question 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

02-07-2012, 05:04 PM	#3
770349688 Junior Member Location: china Join Date: Feb 2012 Posts: 1	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 ？

03-07-2012, 01:56 AM	#5
oxydeepu Member Location: bangalore,india Join Date: Jul 2011 Posts: 41	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

02-07-2012, 04:54 PM	#2
tianyub836 Member Location: China Join Date: Apr 2011 Posts: 23	try option "-m 1"

03-07-2012, 02:03 AM	#6
nilmot13 Member Location: Leeds, UK Join Date: Jan 2011 Posts: 19	Hi Deepak, what exactly are the problems that you are encounting?