SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis. Newsbot! Literature Watch 6 02-06-2012 05:55 AM
RNA-Seq: ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count da Newsbot! Literature Watch 0 11-18-2011 03:20 AM
RNA-Seq: Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Newsbot! Literature Watch 3 07-31-2011 08:08 PM
RNA-Seq: RNA-Seq Analysis of Gene Expression and Alternative Splicing by Double-Rando Newsbot! Literature Watch 0 03-03-2011 03:00 AM
RNA-Seq: RNA-Seq Analysis of Sulfur-Deprived Chlamydomonas Cells Reveals Aspects of A Newsbot! Literature Watch 0 07-01-2010 03:40 AM

Reply
 
Thread Tools
Old 08-21-2011, 06:32 AM   #1
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 106
Default RNA-seq analysis

Hi all,

I am trying to analyze some SOLiD generated RNA-seq data for the first time. Using bwa for the mapping, I have noticed that I am getting between 25-30% of the total reads to map uniquely. This seems like a low number to me but is it what would be expected?

My second question is in regards to trying to identify SNPs from the transcript reads. For this I have been using samtools. For my samples, 75% of the variants that are identified are indels. I am not sure why there are so many indels and could this be due to a problem with the initial alignment?

Thank you all for any help and advice..
lre1234 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 07:31 PM.


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