I'm posting my question here again as you suggested.
I want to build a matrix summarizing methylation levels at CpGs resolution from RRBS data of ENCODE (only from tissues and primary cell, hg19 genome), so that I get the methylation level of every possible CpG covered by one sample (or more). and then download this matrix and save to a file.
what is the easiest way to do it in DeepBlue? in R environment would be the best.
Hi, I'm interested to use DeepBlue to fetch ENCODE metadata based on the accesssion IDs.
Eg. ENCSR000AEH, ENCSR000AEF, ENCSR000AED
This can be done in the package ENCODExplorer but I could not find such features in DeepBlueR. https://www.bioconductor.org/packages/release/bioc/html/ENCODExplorer.html
I'm interested to get gene-level expression counts/TPMs for ENCODE datasets? Can this be done using DeepBlue? For example, there are matrices found here: https://www.encodeproject.org/files/ENCFF833DWB/.
Can these be searched using DeepBlue?
Assuming I want to select different assays for the same set of cell types, or the same assays for the same cell types for different projects. I could create a huge request resulting in one file that I have to split later locally; a more convenient way could be to lock certain selections in the experiment grid and create separate requests.
Select cellA through cellZ (lock)
Select various TFs -> create request
Clear selected TFs
Select various histone modifications -> create request
Clear selected HMs
Select cellA through cellZ (lock)
Select various histone modifications (lock)
Select project A -> create request
Clear project A
Select project B -> create request
I am having some trouble downloading data in the R API/package. It all seems to work fine but I am not getting any signal values. If I download this same data as a bed file there are signals in this range of positon values, but if I download it in R I don't get any values in the signal value column.
id <- deepblue_select_experiments(experiment_name = "E050_WGBS_ReadCoverage.bedgraph", chromosome = "chr6", start=26330464, end=26330664)
request <- deepblue_get_regions(query_id = id, output_format = "CHROMOSOME,START,END,SIGNAL_VALUE")
region <- deepblue_download_request_data(request_id = request)
Called method: deepblue_select_experiments
<span class="ace_constant ace_language">Reported status was: okay Called method: deepblue_get_regions Reported status was: okay Called method: deepblue_info Reported status was: okay Called method: deepblue_info Reported status was: okay trying URL 'http://deepblue.mpi-inf.mpg.de/xmlrpc/download/?r=r791736&key=anonymous_key' Content type 'application/x-bzip2' length 124 bytes ================================================== downloaded 124 bytes Decompressing downloaded file to /tmp/RtmpZfobRp/file495c5e0585df_uncompress Reading file from /tmp/RtmpZfobRp/file495c5e0585df_uncompress </span>GRanges object with 18 ranges and 1 metadata column: seqnames ranges strand | SIGNAL_VALUE <Rle> <IRanges> <Rle> | <character>  chr6 [26330521, 26330522] * |  chr6 [26330522, 26330523] * |  chr6 [26330544, 26330545] * |  chr6 [26330545, 26330546] * |  chr6 [26330552, 26330553] * | ... ... ... ... . ...  chr6 [26330602, 26330603] * |  chr6 [26330603, 26330604] * |  chr6 [26330604, 26330605] * |  chr6 [26330644, 26330645] * |  chr6 [26330645, 26330646] * | ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths
Bedfile downloaded from the web interface open in IGV:
After filtering and clicking on a particular dataset if I want to remove the unwanted data it isn't removing by double clicking even though it is mentioned above as such. Please fix the problem.
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