SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Post-Doc in Milan: miRNAs and non-coding RNAs identification from RNAseq data fnicassi Academic/Non-Profit Jobs 0 08-01-2012 12:54 AM
RNAseq data analysis chknbio Bioinformatics 8 05-24-2012 11:44 PM
[NGS - analysis of gene expression data] Machine Learning + RNAseq data Chuckytah Bioinformatics 7 03-05-2012 03:16 AM
Identification of non-coding RNAs from RNASeq data zee Bioinformatics 1 11-04-2010 05:53 AM
PubMed: Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery Newsbot! Literature Watch 0 09-22-2009 02:00 AM

Reply
 
Thread Tools
Old 10-28-2013, 11:49 PM   #1
afiroz
Member
 
Location: chandigarh

Join Date: Jul 2011
Posts: 14
Question computational SNP Identification/Analysis using RNASeq data

Dear All,

I want to learn SNP Identification/Analysis using RNASeq data, I will be thankful for the computational protocol of the same.
Thanks
afiroz is offline   Reply With Quote
Old 10-29-2013, 12:20 AM   #2
atcghelix
Member
 
Location: CA

Join Date: Jul 2013
Posts: 74
Default

Do you have a reference genome available? If so the below might not be relevant to you.

There are some challenges to SNP discovery in RNA-seq data that are still being worked out, as far as I know, especially when you don't have a reference genome. Basically, when you assemble RNA-seq data you expect to get many different isoforms of the same gene. These isoforms are sometimes grouped with paralogues which can be difficult to distinguish from isoforms. When it comes time to calling SNPs, you want to find some way to reduce the redundancy of the de novo assembly to more accurately represent the underlying biology of a single genomic origin for multiple transcripts. If you simply cluster using something like CD-hit-est this will do things like collapse paralogues too.

This doesn't mean it's impossible, and I'd love to hear others' input. I'm trying to do this in a few species with no close reference genomes as well.

I've found this paper to be helpful: http://onlinelibrary.wiley.com/doi/1...998.12077/full
atcghelix is offline   Reply With Quote
Old 10-29-2013, 02:38 AM   #3
afiroz
Member
 
Location: chandigarh

Join Date: Jul 2011
Posts: 14
Default

Thanks for reply... yes If having reference genome..... what would be the protocol for the SNP identification and analysis... also which tools is most useful for same. thanks again for valuable response/reply.
firoz
afiroz is offline   Reply With Quote
Old 10-29-2013, 12:34 PM   #4
atcghelix
Member
 
Location: CA

Join Date: Jul 2013
Posts: 74
Default

Do you know where your exon junctions are for your genome?
atcghelix is offline   Reply With Quote
Old 10-29-2013, 01:19 PM   #5
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
Default

Quote:
Originally Posted by afiroz View Post
Thanks for reply... yes If having reference genome..... what would be the protocol for the SNP identification and analysis... also which tools is most useful for same. thanks again for valuable response/reply.
firoz
You may try the Subread package which includes an aligner (subjunc) that performs full alignments of RNA-seq reads and also a SNP caller (exactSNP).
shi is offline   Reply With Quote
Old 10-29-2013, 09:29 PM   #6
afiroz
Member
 
Location: chandigarh

Join Date: Jul 2011
Posts: 14
Default

Dont know the exon junction
afiroz is offline   Reply With Quote
Old 10-30-2013, 01:15 AM   #7
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
Default

You dont need to know the exon junctions. The aligner will detect them for you.
shi is offline   Reply With Quote
Old 10-30-2013, 01:26 AM   #8
afiroz
Member
 
Location: chandigarh

Join Date: Jul 2011
Posts: 14
Default

Thanks for valuable reply. am trying subread packege (aligner) and will let u know further.. thanks again
afiroz 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 03:04 PM.


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