Go Back   SEQanswers > Applications Forums > Genomic Resequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
DNA contamination in mRNA seq prepare ccqqsunshine Sample Prep / Library Generation 3 04-18-2012 07:09 PM
no effect for picard cleansam liuxq Bioinformatics 0 12-29-2011 09:26 PM
Batch effect, SNPs YKay Genomic Resequencing 0 12-13-2011 05:42 AM
BWA parameters for mRNA-seq aligning against mRNA refseq kwicher SOLiD 1 09-19-2011 03:45 AM
Samtools seek like effect. malavv Bioinformatics 1 07-07-2011 12:55 AM

Thread Tools
Old 08-23-2011, 09:43 PM   #1
Junior Member
Location: Canada

Join Date: Aug 2011
Posts: 3
Default effect of mRNA contamination

We have sequenced some yeast strains with very high coverage (~30x). However, seems like our samples were contaminated with mRNA. Seems like we have much more coverage at coding sites. Before doing any downstream analysis, I would like to know what kind of (hidden)side effects would this cause in terms of (a) coding snp calling, (b) non-coding snp calling, and (c) de-novo assemly and structural variant calling ? Do you guys think it is garbage and we should re-sequence or we might still do something with it?
eren 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 03:37 PM.

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