I would like to do TFRN (Transcription factor regulatory network) analysis and I need DNase-seq bam files for cancer cell lines. I know the ENCODE but I need this information for other cell lines which ENCODE doesn't have it. So, anybody know a source to download DNase-seq bam files, except ENCODE?
Hello Elyas
I guess the only public file can be found at https://www.ncbi.nlm.nih.gov/bioproject/PRJEB9956. This is not a Bam file unfortunately. You may look for this accession in the Galaxy server for its Bam file.
Good luck
Hello Elyas,
You can search it through PubMed, then download the related files using GEO/SRA. Finding the .bam file is usually a bit difficult because most of the data (DNase-seq) are published as RAW data or called peak data (.txt).
You can also search for the ATAC-seq data which are related to open chromatin regions like DNase-seq.
Ali Javadmanesh
Soheil Yousefi
Thank you very much for your helpful answers.
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