Question: Bowtie2 alignment help for ATAC-seq
0
gravatar for mrs.whirly
10 weeks ago by
mrs.whirly0
mrs.whirly0 wrote:

Hello,

I am trying to align my raw sequencing data using bowtie2. This is for ATAC-seq analysis. What are the best commands settings to use on bowtie for that? I know I want paired-end alignments and local sequencing, but I am not sure what other options are good for ATAC-seq, such not including discordant pairs, limitations to concordant pairs (e.g. orientation, distance etc.), or anything else! Any advice is appreciated!

Thanks,

ADD COMMENTlink modified 9 weeks ago by ATpoint26k • written 10 weeks ago by mrs.whirly0

How about leaving everything else as the default and then just taking a look at the results. As a rule of thumb, it's best to start with more-or-less default settings on tools and then tweak settings further only after having a look at the results.

ADD REPLYlink written 10 weeks ago by Devon Ryan93k
0
gravatar for ATpoint
9 weeks ago by
ATpoint26k
Germany
ATpoint26k wrote:

Leaving everything at default is just fine expect that I find --very-sensitive and -X 2000 helpful. --very-sensitive simply triggers a more sensitive alignment mode and -X 2000 will flag reads with TLEN up to 2kb as concordant, still I doubt this will have a notable effect compared to the defaults which are always a good starting point.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by ATpoint26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 762 users visited in the last hour