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 > wgEncodeDukeAffyExonUrotsaUt189SimpleSignalRep1 > > Possible Cell Lines > Urothelia > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
