Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
high levels of broken read pairs? gevielr Bioinformatics 1 07-09-2014 02:52 PM
Dealing with overlapping read pairs Jeremy37 Bioinformatics 7 03-24-2013 04:03 PM
Tophat can't find read-pairs?? all_your_base Bioinformatics 2 12-17-2012 09:35 PM
Tools to identify read pairs? Kennels Bioinformatics 1 04-30-2012 09:48 PM
Simulate Illumina read-pairs gene coder Bioinformatics 4 07-07-2011 04:37 AM

Thread Tools
Old 01-08-2019, 04:01 PM   #1
Junior Member
Location: San Francisco, CA

Join Date: Aug 2015
Posts: 7
Default read pairs to fragment coordinates

Hi All,

I have a bam file from the alignment of paired-end NGS data to the human genome. Most of these read-pairs are non-overlapping. Is there any tool that takes this bam as input and provides the merged coordinates from the pairs.

Read1-FWD: chr1 1 20
Read1-REV: chr1 80 100

Result: chr1 1 100

If only one read is aligned, then ignore its mate. If the alignment is on opposite strand, reverse for that.

I know a lot of tools estimate fragment size, but do they output results like above as well? I can write a quick script for this, but was wondering if something was already available.
Many thanks.
touchsk is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:11 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO