Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
MG-RAST - remove or retain non-overlapping paired-end reads rhinoceros Metagenomics 0 08-05-2013 04:31 AM
Remove paired end duplicated reads -Samtools-Picard paolo.kunder Bioinformatics 2 02-11-2013 08:55 AM
Does Tophat remove duplicates aquleaf Bioinformatics 1 01-07-2013 02:47 PM
What is the differences between pre-filtering vs PCR duplicates remove mapped reads? yksikaksi SOLiD 4 04-18-2012 11:47 PM
set up TOPHAT run with paired end reads PFS Bioinformatics 1 03-08-2011 04:45 PM

Thread Tools
Old 12-16-2014, 06:14 PM   #1
Junior Member
Location: Los Angeles, CA

Join Date: Aug 2011
Posts: 2
Question To remove or to keep duplicates in alignment of NGS paired reads to a set of contigs

I have a SAM file containing alignments of NGS paired reads against a set of assembled contigs (de novo).

If I might need to infer some information about the coverage of these contigs from the SAM file (e.g. inferring that contigs are unique ones or collapsed repeats with some copy numbers (repeat counts) in the genome), should I mark and remove duplicates either from SAM file (using Picard MarkDuplicates or SAMtools redup) or from reads sequences (FastUniq) or just keep everything as it is to not loose anything important that might affect downstream analyses?

Would you please share your opinion with me and let me know pros and cons of duplicate removal in this case?

misagh is offline   Reply With Quote

contigs, duplicates, paired reads, sam/bam alignment

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 01:05 PM.

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