BS-Seq Public /Sharing Data

zee · 01-21-2009, 12:41 AM

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?

zee · 01-21-2009, 08:09 PM

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?

forrest · 08-05-2011, 12:38 PM

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

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01-21-2009, 12:41 AM	#1
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	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; 01-21-2009 at 12:47 AM.

01-21-2009, 08:09 PM	#2
zee NGS specialist Location: Malaysia Join Date: Apr 2008 Posts: 249	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?

08-05-2011, 12:38 PM	#3
forrest Junior Member Location: Madison, WI Join Date: Sep 2009 Posts: 2	I don't how to convent these bin files to fastq/fasta file? Any one know how to do this? Thanks so much.