Question: [Genome] Genome-Wide Dataset Of Protein Location Conversion
gravatar for Manuel Leichsenring
8.3 years ago by
Manuel Leichsenring20 wrote:
Hi Dana, the way I do it, is the following: Get a list of all genes (e.g. RefSeq) using the "Get Data" "From UCSC Main Tablebrowser" option. "Get Flanks" of the genes (in your case 1kb or 5kb). Use "Join" from "Operate on genomic intervals" to intersect your peak regions with a) Upstream Flanks b) Downstream Flanks c) the genes themselves. You can then use the "Group" option and "Concatenate queries" to get a single list of genes without duplicates. Cheers Manuel Good Afternoon Dana: You could produce such a list from a given position with a MySQL operation to the UCSC public MySQL server. Note this Wiki page with a description of the command: --Hiram To: Subject: [galaxy-user] FW: [Genome] Genome-wide dataset of protein location conversion Hello, We have been trying to determine a method to convert ChIP-Seq coordinates into a list of genes and are wondering the best way to utilize the Galaxy browser. The UCSC folks suggested you could help but I should have been more specific with my request. Ideally we would like to take global binding coordinates and find out what genes are nearby (ie at either a 1 or 5kb) instead of simply the “closest feature”. Might you be able to advise on this? I have enclosed the text (.bed format) file I used to get the binding sites in the UCSC genome browser. Thanks in advance! Cheers, Dana _______________________________________________ galaxy-user mailing list -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren:
chip-seq • 965 views
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