Public Mouse Methyl-seq Data?

[serenaliao]

Hi everyone,

I am looking for a public whole genome methyl-seq data, GA or hiseq to do comparison to another platform. I have actually looked into one data deposit to GEO, but it turns out their bam file has a mixture of single and pair-end data(about 70% single end), is that very strange?

Actually I have no idea how to proceed with that. Does anyone have any idea or suggestion to any other public data?

Thanks in advance!

[simonandrews]

We have deposited quite a bit of this type of data, both MeDIP and BS-Seq/RRBS. Our data all went into EBI SRA. There's a list of them at:

http://www.ebi.ac.uk/ena/data/search?query=babraham

[serenaliao]

We have deposited quite a bit of this type of data, both MeDIP and BS-Seq/RRBS. Our data all went into EBI SRA. There's a list of them at:

http://www.ebi.ac.uk/ena/data/search?query=babraham

Thanks, I will try those.

[serenaliao]

We have deposited quite a bit of this type of data, both MeDIP and BS-Seq/RRBS. Our data all went into EBI SRA. There's a list of them at:

http://www.ebi.ac.uk/ena/data/search?query=babraham

Hi andrew,

I downloaded two samples BS from EBI SRA. Basically, we are more interesting in Hiseq2000. I am wondering if you can answer my question. After I download sample DRR001680, I found the reads are all "N". That's very wired, isn't it? Both of the two samples and pair-end reads are like this. Did I miss anything. Appreciate your help!

@DRR001680.48 HWI-ST325_154:5:100:2302:1074/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Or any other one who have experience dealing with ENA data is welcome to give suggestions!

[simonandrews]

I downloaded two samples BS from EBI SRA. Basically, we are more interesting in Hiseq2000. I am wondering if you can answer my question. After I download sample DRR001680, I found the reads are all "N". That's very wired, isn't it? Both of the two samples and pair-end reads are like this. Did I miss anything. Appreciate your help!

It's quite common for the sequences at the start of an illumina file to be all Ns. They're normally from the tiles at the edge of the flowcell where the data can be pretty poor. You don't have to scroll far into the file to see real sequence show up. Trying to browse a fastq file is often pretty fruitless as you'll get bored of scrolling before you've got far enough into the file to see representative sequences.