Roadmap WGBS methylation data download

Hi All,

Is there any easy way to download all the WGBS data (Bam or Wig) of Roadmap project?

I'd like to have a FTP or Wget weblinks.

Thanks.

roadmap epigenome wgbs rrbs

• 2,740 views • link

updated 9.6 years ago by tim.triche •

• written 10.0 years ago by Shicheng Guo

1 answer

WIGs and SRA: https://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/?search=bisulfite&display=181

FASTQs (example for CD14+ WGBS from the Broad within the REMC project): http://www.ebi.ac.uk/ena/data/view/SRR1104848

Plan on plugging in the SRR/SRX numbers for the ENA template individually, but it's still faster than using slowq-dump.

• 0 views • link

written 9.6 years ago by tim.triche •

More posts like this

MD5Sums of fastq files from SRA
written 4.5 years ago by ildem •

Hi all, I downloaded a bunch of fastq files using wget. i.e. wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/072/SRR13198172/SRR13198172.fastq.gz I did this because SRA download was either failing or taking …
NDEx database data download
written 5.2 years ago by Shicheng Guo

Is there any way to download NDEx data with bash script. I want to download all pathways from this database. http://public.ndexbio.org/#/ Thanks.
How to decrease the number of candidate TFs binding to gene promoter region
written 6.5 years ago by Shicheng Guo

Hi All, I want to know which transcript factors regulated gene expression of FGF6. Therefore, I used all the ChIP-seq data for 685 TFs from …
GTF annotation for Staphylococcus aureus
written 6.6 years ago by Shicheng Guo

Hi All, Where to download [GTF][1] annotation to staphylococcus aureus? Thanks. [1]: https://useast.ensembl.org/info/data/ftp/index.html
McGill Epigenomics Mapping Centre BS-Seq Data Problem
written 8.0 years ago by Shicheng Guo

Hi All, I tried to download some BS-Seq data from [McGill Epigenomics Mapping Centre (\[Here Database Link\]\[1\])][1] I have a little assumption about the BS-Seq …
How to create a FTP link which can be downloaded by 'wget' command?
written 8.3 years ago by xuling2015 •

I have a 30Gb fasta file. I'd like to upload it to IMG/ER, but they asked me to provide a FTP link (with the link, …
Roadmap Epigenomcis: Sample collection and detail sample type information
written 9.8 years ago by Shicheng Guo

Hi, When I download Roadmap Epigenomcis dataset, I know STL-0002-Lung is the normal lung tissues from STL-0002 individual, but do you know How can I …
Roadmap Epigenomics Project Sample Amalgamation of Same Tissue?
written 10.2 years ago by Shicheng Guo

Hi All, I download the 5mC methylation (WGBS) data from Roadmap Epigenomics Project. However, I found only 37 column were existed in the FractionMethylation (fm) …
Low methylation regions or non-methylation regions from WGBS dataset
written 10.5 years ago by Shicheng Guo

Hi All, Any method or software to recommend to identify low methylation regions or non-methylation regions from WGBS dataset? 1. swDMR 2. MethylSeekR Thanks
The best data format for to store BS-seq or RRBS dataset
written 10.7 years ago by Shicheng Guo

Hi All, Is there any suggestion which kind of intermediate data format would be nice to be use to save the BS-seq or RRBS dataset? …