Great Katrina! Thank you very, very much. Regards, Diego El día 14 de febrero de 2012 19:26, Katrina Learned <[email protected]> escribió: > Hi Diego, > > If you only have table names, probably the fastest thing to do is to go to > the download directory for each of the composite (i.e. parent) tracks > (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/) where you'll > find a files.txt file. This file lists all the files in the composite track > and each file's associated metadata. While you won't find the table listed, > you will see a file with the same name (at least up to the file type > suffix). One of the metadata items included is cell, which will provide the > name of the cell line. Here are the direct links to the files.txt for the > last two you were having trouble with: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/files.txt > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/files.txt > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeDukeAffyExon/files.txt > > You'll find that some of the Astrocy tables have been renamed NH-A because > both were representing the same cell line. Keratinocyte is another name for > NHEK. For more info on NH-A and NHEK, see the ENCODE human cell types page: > http://genome.ucsc.edu/ENCODE/cellTypes.html > > Please contact the mail list ([email protected]) again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > > On Tue Feb 14 15:24:09 2012, Diego Pereira wrote: > > > Good afternoon, > I think I could classify well most of the tables, but still there are > 2 "terms" I cannot assign to an specific cell type: > "Astrocy" > "Keratinocyte" > Can you give me a hand with this? > Thanks, > Diego > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > On 2/13/12 4:55 PM, Diego Pereira wrote: > > Dear all, > I'm having some difficulties in classifying the following tables > according to their cell type. > I divided them into 2 groups: > Group 1 are tables that can belong to more than 1 cell type. Can you > please tell me to which cell type they refer to? > For Group 2 tables I would like to ask you to confirm that the > "possible cell line" is actually the cell type those tables refer to. > In case the actual cell type is different from those I labeled as > "Possible Cell Lines", can you please let me know what is the actual > cell type? > > Thanks in advance, > Diego > > > Group 1 > > Term "Hpae" > > Tables > wgEncodeHaibMethylRrbsHpaeUwSitesRep1 > wgEncodeHaibMethylRrbsHpaeUwSitesRep2 > wgEncodeHaibMethylRrbsHpaeUwstamgrowprotSitesRep1 > wgEncodeHaibMethylRrbsHpaeUwstamgrowprotSitesRep2 > wgEncodeHaibMethyl450HpaeSitesRep1 > > Possible Cell Lines > HPAEC > HPAEpiC > > Term "Panis" > > Tables > wgEncodeOpenChromDnasePanisdPk > > Possible Cell Lines > PanIsletD > PanIslets > > Term "Astrocy" > > Tables > wgEncodeOpenChromFaireAstrocyPk > wgEncodeDukeAffyExonAstrocySimpleSignalRep1 > wgEncodeDukeAffyExonAstrocySimpleSignalRep2 > > Possible Cell Lines > HA-h > HA-sp > HAc > NH-A > U87 > > Group 2 > > Term "Keratinocyte" > > Tables > wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongnonpolya > wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongpolya > wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongnonpolya > wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongpolya > wgEncodeAffyRnaChipTransfragsKeratinocyteCytosolLongnonpolya > wgEncodeAffyRnaChipTransfragsKeratinocyteCytosolLongpolya > wgEncodeAffyRnaChipTransfragsKeratinocyteNucleusLongnonpolya > wgEncodeAffyRnaChipTransfragsKeratinocyteNucleusLongpolya > > Possible Cell Lines > NHEK > > Term "H7es" > > Tables > wgEncodeUwDgfH7esPkV2 > wgEncodeUwDnaseH7esPkRep1V2 > wgEncodeUwDnaseH7esPkRep2 > wgEncodeUwHistoneH7esH3k27me3StdPkRep1 > wgEncodeUwHistoneH7esH3k27me3StdPkRep2 > wgEncodeUwHistoneH7esH3k36me3StdPkRep1 > wgEncodeUwHistoneH7esH3k36me3StdPkRep2 > wgEncodeUwHistoneH7esH3k4me3StdPkRep1 > wgEncodeUwHistoneH7esH3k4me3StdPkRep2 > wgEncodeUwDgfH7esHotspots > wgEncodeUwDnaseH7esHotspotsRep1 > wgEncodeUwDnaseH7esHotspotsRep2 > wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 > wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 > wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep1 > wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep2 > wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep1 > wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep2 > wgEncodeUwAffyExonArrayH7esSimpleSignalRep1 > wgEncodeUwAffyExonArrayH7esSimpleSignalRep2 > > Possible Cell Lines > H7-hESC > > Term "Urotsa" > > Tables > wgEncodeOpenChromDnaseUrotsaPk > wgEncodeOpenChromDnaseUrotsaUt189Pk > wgEncodeOpenChromFaireUrotsaPk > wgEncodeOpenChromFaireUrotsaUt189Pk > wgEncodeDukeAffyExonUrotsaSimpleSignalRep1 > wgEncodeDukeAffyExonUrotsaUt18 > 9SimpleSignalRep1 > > Possible Cell Lines > Urothelia > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome
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