SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Understanding sequence alignment bio_informatics General 2 09-20-2014 06:08 AM
Understanding Mauve Contig MOver Alignment Result chariko Bioinformatics 0 08-28-2014 08:59 AM
Conceptual question of validity of transcriptional profiling Mike2188 General 1 04-18-2014 02:11 PM
[algorithm] Help understanding substring chaining for spliced gene alignment gumbit Bioinformatics 5 05-21-2013 07:08 PM
Removal of poor quality reads before alignment gibsongenetics Bioinformatics 2 05-16-2011 06:22 AM

Reply
 
Thread Tools
Old 03-24-2015, 08:08 PM   #1
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Conceptual Poor Alignment Understanding

Hello.
I am working on some RNAseq and received a few poor reads from our sample set. One possible undersatnding is cDNA contamination. note we aligned untrimmed reads because if there is "junk" in the read, then it will not align to the reference genome and automatically become omitted.

well what other possibilities could this be? My troubleshoot workaround is to trim the reads for quality and omit the adapters. Is it possible for adapter contamination in the prep kit?

if we remove the low quality reads, this might remove the entire read, or will it?

How has your team interpreted poor aligned reads? I will do a quality analysis to understand why the reads were mal-aligned. what are common things to look for?
arcolombo698 is offline   Reply With Quote
Old 03-24-2015, 09:31 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

FastQC is a pretty good tool for looking at raw data, and it is often helpful if you have a problematic library to run FastQC and attach the pdf output to your post, so other people can look at it. If the FastQC graphs look normal the problem may be contamination.

I don't recommend aligning non-adapter-trimmed RNA-seq reads, as that will incur bias (against short transcripts, for example). For contamination detection, a good approach is to map the reads to the reference at high sensitivity, then take a subset of the unaligned reads and map them to a broad dataset such as nt to see what they hit.
Brian Bushnell is offline   Reply With Quote
Reply

Tags
alignment, quality

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 02:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO