SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is there any public raw intensity data from RNA-Seq endether Bioinformatics 0 10-10-2011 08:06 AM
Public repositories for NGS data greener Bioinformatics 1 05-02-2011 12:42 PM
public data sets muchomaas Bioinformatics 2 06-08-2010 01:48 AM
public paire end (mate pair) transcriptome data set? iqc Bioinformatics 2 11-12-2009 12:18 PM
Public Helicos Data zee Bioinformatics 2 08-11-2008 08:14 PM

Reply
 
Thread Tools
Old 01-20-2009, 11:41 PM   #1
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default BS-Seq Public /Sharing Data

Hi,

Does anybody know of a source of public BS-Seq data to validate methylation alignment on?
I'm looking for SEQ-PRB/FASTQ formatted short reads from the Illumina GA platform.

I found the Cokus dataset at http://epigenomics.mcdb.ucla.edu/BS-Seq/download.html but I cant make head or tail of what's in there or how to get at the actual reads. Can anybody help?

Last edited by zee; 01-20-2009 at 11:47 PM.
zee is offline   Reply With Quote
Old 01-21-2009, 07:09 PM   #2
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

I decompressed the Cokus et al., 2008, data and obtained a whole lot of directories and C programs. I cant run the C programs because I dont have a license for Matlab.

Anybody know what to do with these :

N1try2-L7-sig2_T-17.littleEndianDoubles.bin
N1try2-L7-sig2_T-18.littleEndianDoubles.bin
N1try2-L7-sig2_T-19.littleEndianDoubles.bin
N1try2-L7-sig2_T-20.littleEndianDoubles.bin
N1try2-L7-sig2_T-21.littleEndianDoubles.bin
N1try2-L7-sig2_T-22.littleEndianDoubles.bin
N1try2-L7-sig2_T-23.littleEndianDoubles.bin
N1try2-L7-sig2_T-24.littleEndianDoubles.bin
N1try2-L7-sig2_T-25.littleEndianDoubles.bin
N1try2-L7-sig2_T-26.littleEndianDoubles.bin
N1try2-L7-sig2_T-27.littleEndianDoubles.bin
N1try2-L7-sig2_T-28.littleEndianDoubles.bin
N1try2-L7-sig2_T-29.littleEndianDoubles.bin
N1try2-L7-sig2_T-30.littleEndianDoubles.bin
N1try2-L7-sig2_T-31.littleEndianDoubles.bin
N1try2-L7-sig2_T-32.littleEndianDoubles.bin
N1try2-L7-sig2_T-33.littleEndianDoubles.bin
N1try2-L7-sig2_T-34.littleEndianDoubles.bin
N1try2-L7-sig2_T-35.littleEndianDoubles.bin
N1try2-L7-sig2_T-36.littleEndianDoubles.bin


Are these the raw images from the Illumina machine and how do I produce some reads from this?
zee is offline   Reply With Quote
Old 08-05-2011, 11:38 AM   #3
forrest
Junior Member
 
Location: Madison, WI

Join Date: Sep 2009
Posts: 2
Default

I don't how to convent these bin files to fastq/fasta file? Any one know how to do this? Thanks so much.
forrest 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 12:17 PM.


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