Question: Are the ENCODE raw fastq files and genotyping data available for each cell line?
gravatar for Milos Pjanic
3.4 years ago by
Milos Pjanic30
Stanford University
Milos Pjanic30 wrote:

I would like to check allele specific mapping of reads from the ENCODE ChIP-Seq data to a specific enhancer SNP in lines that are heterozygotes. Are the imputed genotypes available for ENCODE cell lines? Or alternatively raw fastq files from the ENCODE ChIP-Seq, as I could use ChIP-Seq fastqs to call variants.

chip-seq encode • 1.1k views
ADD COMMENTlink modified 3.4 years ago by Khader Shameer18k • written 3.4 years ago by Milos Pjanic30
gravatar for Khader Shameer
3.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Yes - detailed lists are here and here.

  • FASTQ is available from SRA
  • Genotyping data from GEO
ADD COMMENTlink written 3.4 years ago by Khader Shameer18k
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