SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cutting corners with Illumina Sample Prep Rocketknight Sample Prep / Library Generation 21 03-29-2013 11:17 AM
typical parameters for filtering Illumina RNASEQ reads PFS Bioinformatics 1 09-09-2011 10:42 AM
RNAseq sample files ocs Bioinformatics 5 07-29-2011 04:40 PM
Why are Illumina paired-end SRA datasets made up of 3 FASTQ files? Bio.X2Y Illumina/Solexa 9 12-21-2010 12:36 PM
Over represesented tags at 3'UTR - Illumina RNAseq aldenk RNA Sequencing 2 04-09-2010 01:06 PM

Reply
 
Thread Tools
Old 08-10-2011, 07:55 AM   #1
hmortens
Member
 
Location: RTP

Join Date: Aug 2011
Posts: 12
Default sample Illumina RNAseq datasets

hi,
I am attempting to start a workflow setup for RNAseq analyses. I would like to get a hold of a reasonably sized Illumina RNAseq dataset to do some data transfer tests and tests some of the alignment tools out there. Was thinking to use Pickrell, 2010. How big is 'reasonable'? are the raw files FASTQ? and does anyone have a suggestion on an available human dataset to play around with?
thanks,
hmortens
hmortens is offline   Reply With Quote
Old 04-10-2012, 07:29 PM   #2
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

This can be a good starting point for you: http://seqanswers.com/wiki/How-to/RNASeq_analysis

Do start with around 30 - 50 million reads to do useful analysis
__________________
--
bioinfosm
bioinfosm is offline   Reply With Quote
Old 04-11-2012, 06:10 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,069
Default

http://sra.dnanexus.com/?result_type...show=&q=RNAseq

Filter on the instrument type using the left column.
GenoMax is offline   Reply With Quote
Old 04-11-2012, 08:07 AM   #4
sidderb
Member
 
Location: Cambridge UK

Join Date: Aug 2011
Posts: 14
Default

i have found the illumina bodymap2 data to be a good test set. This includes multiple formats (SE/PE) from 16 human tissues.

http://www.ebi.ac.uk/arrayexpress/br...g&expandefo=on
__________________
@sidderb
sidderb is offline   Reply With Quote
Reply

Tags
fastq, illumina, rnaseq, sample datasets

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 12:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO