Ask Your Question
0

export information on sequence reads

asked 2019-06-24 10:55:15 -0600

this post is marked as community wiki

This post is a wiki. Anyone with karma >75 is welcome to improve it.

Hi,

We are studying the rate of de novo mutagenesis after genetic engineering. We have deep-sequenced a target region of 2kb and are interested to know how many mutations have been generated and at what percentage. I understand we can click on a specific nucleotide and obtain from the data console the read information. Is there a way that I can obtain the collective read information for each nucleotide of the whole 2kb region without having to click on each of them one by one?

edit retag flag offensive close merge delete

1 answer

Sort by ยป oldest newest most voted
0

answered 2019-06-28 10:28:12 -0600

Gabe Rudy gravatar image

No, GenomeBrowse does not have an output that represents the per-base pileup information of a whole region.

The samtools mpileup tool may provide the type of output you are looking for

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

Follow
1 follower

subscribe to rss feed

Stats

Asked: 2019-06-24 10:55:15 -0600

Seen: 699 times

Last updated: Jun 28 '19

Related questions

"Current filters hide all data sources"

Copyright Goldenhelix, 2012-2015.
Powered by Askbot version 0.7.51