SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
mpileup multiple samples - individual DP4/AF1 values catriona Bioinformatics 3 07-22-2014 03:49 PM
Cuffdiff with biological replicates vs individual samples not adding up. Noa Bioinformatics 0 07-02-2013 10:50 PM
TopHat2 run on individual or multiple samples adumitri Bioinformatics 12 05-17-2012 02:12 PM
How to define a expressed gene based on RNA-seq data zeam RNA Sequencing 6 07-11-2011 01:27 PM
How to separate individual sample variants from multiple samples meher Bioinformatics 0 06-30-2011 12:11 PM

Reply
 
Thread Tools
Old 08-19-2013, 02:50 AM   #1
dietmar13
Senior Member
 
Location: Vienna

Join Date: Mar 2010
Posts: 107
Default define if two RNA-seq samples from one individual

hello,

i have two RNA-seq libraries (~10 mio 50 PE) from tumor cells and i want to know if these are from the same person.

which is the easiest way to do this. as control i have other RNA-seq libraries from other persons...

thank you in advance,

dietmar
dietmar13 is offline   Reply With Quote
Old 08-19-2013, 03:17 AM   #2
alec
Member
 
Location: Cambridge, MA

Join Date: Apr 2011
Posts: 18
Default

You could compare their SNPs. The number of differences due to somatic mutations should be relatively small, and you could filter out any that aren't in dbSNP. You'll also want to filter out cases where a SNP is called in one sample but not in another because the gene expression is too low. A program like SomaticSniper that directly compares two bam files might be the best way to go.
alec is offline   Reply With Quote
Old 08-19-2013, 03:24 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,062
Default

If you also had independent SNP chip data then it would be a good control to compare.
GenoMax is offline   Reply With Quote
Old 08-19-2013, 11:07 PM   #4
dietmar13
Senior Member
 
Location: Vienna

Join Date: Mar 2010
Posts: 107
Default

@alec,

SomaticSniper would be the perfect answer, but unfortunately i get no results for either a same-individual pair or a different-individual pair...

the program seems to work - i get no errors - but the output-file is empty.

perhaps this program works only with exom or genomic data, not with RNA-seq data?

knows someone else a similar (easy usable) program especially for RNA-seq data. i don't want to implement a complete SNP analysis pipeline...
dietmar13 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 07:02 PM.


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