Question: Aligning using Bowtie2
gravatar for kshitijtayal
2.6 years ago by
kshitijtayal30 wrote:

I am using Bowtie2 to align the reads to lambda_virus genome using the following command.

./bowtie2 -x lambda_virus -U example/reads/reads_1.fq -S eg1.sam

It shows following output in the console i.e. 10000 reads; of these: 10000 (100.00%) were unpaired; of these: 596 (5.96%) aligned 0 times 9404 (94.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times 94.04% overall alignment rate

I want to relax the edit distance parameter so that each and every read can get aligned. Can somebody suggest how to do it in bowtie. Also i want the set of reads that get perfectly aligned with 0 edit distance. How to do that in bowtie. I tried reading the manual but it is using all the biological definitions and i am myself from computer science background.

Thanks in advance,

alignment forum bowtie2 • 1.4k views
ADD COMMENTlink modified 2.6 years ago by Carambakaracho970 • written 2.6 years ago by kshitijtayal30

If you want to align all reads, I suggest you use BBMap, which is a more sensitive aligner, with the "slow" flag. BBMap also can give you the perfectly aligned reads like this: ref=lambda.fa in=reads.fq outm=mapped.sam perfectmode

But, it's possible that the reads that don't align are not aligning for a reason. They might not be from Lambda, for example. Or, you might need to do adapter-trimming first.

ADD REPLYlink written 2.6 years ago by Brian Bushnell16k
gravatar for Carambakaracho
2.6 years ago by
Carambakaracho970 wrote:

bowtie2 has very stringent alignment parameters. However you can control them a bit via the D, R N, L and i options. Try to set N to a higher value

ADD COMMENTlink written 2.6 years ago by Carambakaracho970

@Carambakaracho Max value that i can set for N is 1. Is there any other possible way ? Description for -N <int>- Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0.

ADD REPLYlink written 2.6 years ago by kshitijtayal30

@kshitijtayal ok, I never tried it myself, the description suggests that values beyond 1 might be possible. In case reducing the seed length toghether with allowing mismatches is not successful, give Brian Bushnell's suggestion BBMap a try

ADD REPLYlink written 2.6 years ago by Carambakaracho970
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1381 users visited in the last hour