Question: Bowtie2 alignment help for ATAC-seq
0
gravatar for mrs.whirly
6 months 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 6 months ago by ATpoint32k • written 6 months 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 6 months ago by Devon Ryan94k
0
gravatar for ATpoint
6 months ago by
ATpoint32k
Germany
ATpoint32k 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 6 months ago • written 6 months ago by ATpoint32k
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