SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Removing duplicates is it really necessary? foxyg Bioinformatics 34 12-02-2016 01:17 PM
Samtools flagstat - no duplicates? Orr Shomroni Bioinformatics 3 11-25-2011 12:46 AM
Find the segemntal duplicates ardmore Bioinformatics 10 11-10-2011 06:21 AM
cufflinks errors of duplicates middlemale Bioinformatics 3 10-25-2010 05:01 AM
26% duplicates KevinLam Bioinformatics 4 08-19-2010 04:20 PM

Reply
 
Thread Tools
Old 02-15-2011, 01:00 PM   #1
hlmeng
Junior Member
 
Location: USA

Join Date: Feb 2011
Posts: 1
Default Read Duplicates

I used picard tools to mark the duplicates in .bam file. But I want to know more about those duplicates in .bam file. For example, what is the frequency distribution of duplicates with different length? Is there any easy way to do that? Is there any tools can walk through .bam/.sam file to get that information?

Thanks.
hlmeng is offline   Reply With Quote
Old 02-15-2011, 06:17 PM   #2
asangqi
Junior Member
 
Location: usa

Join Date: Feb 2011
Posts: 4
Default

this may help you:
http://samtools.sourceforge.net/samtools.shtml

rmdup samtools rmdup [-sS] <input.srt.bam> <out.bam>

Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).

OPTIONS:
-s Remove duplicate for single-end reads. By default, the command works for paired-end reads only.
-S Treat paired-end reads and single-end reads.
asangqi is offline   Reply With Quote
Reply

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 07:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO