Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
'Properly paired' reads in sam flag from TopHat mapping AdamB Bioinformatics 9 03-08-2012 08:30 AM
How to check if reads are properly paired in mate-pair data? genepool_bee Bioinformatics 2 02-22-2011 02:07 AM
samtool fixmate drastically decreases the number of properly paired reads Jerry-cs Bioinformatics 1 01-13-2011 06:04 AM
properly paired reads in TopHat output shurjo Bioinformatics 2 12-02-2010 12:35 PM
queston for count of properly-paired end jlfmssm Bioinformatics 6 07-06-2010 09:07 AM

Thread Tools
Old 05-24-2011, 03:01 PM   #1
Location: Italy

Join Date: Feb 2011
Posts: 16
Question Help me!!!!! low % of properly paired reads!!!

Hi all,
I have an important question:
I have 75x2 reads from Illumina HiScan and I preformed:

-alignment with TopHat
-samtools flagstat to know the % of properly paired reads

This % very low, around 1% for all samples........why???

I have also increased the -r option (mate inner dist), from 85 to 1000 but there're no significant differences!

My only ipothesis of these situation is a very low quality of reverse strand because during the run we had problem with enzyme and the boxplots of reverse reads had low quality associated value. Is it possible??? Low quality of reverse strand reads can influence the % of properly paired reads??

I think also that downstream analysis are compromised......Help me please if sameone knows this situation!
Trudy is offline   Reply With Quote
Old 05-25-2011, 12:26 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

Assuming you're aligning to genomic sequence then any pairs which fall into different exons (which will probably be quite a lot of them), will have effective inner distances much bigger than 1kb due to the added size of the introns you'll be spanning.

Looking at mate pair distances on the genome doesn't make much sense for RNA-Seq data. If your improper pairs come from the pairs mapping to the same strand, then that's cause for concern, but as long as your pairs fall into the same gene then for RNA-Seq that's probably enough.
simonandrews 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 08:23 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO