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Old 09-25-2013, 03:20 AM   #1
ge2sasag
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Location: Stockholm

Join Date: Apr 2013
Posts: 42
Default which files to use from already-analysed ENCODE RNA-seq data?

Hi all, Im newbie in RNA-seq so I hope someone can help

I need to use the information from two RNA-seq data from ENCODE but there are several file types that I can use:

GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Il200ExonsGencV3cRep1V3
GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Il200GeneDeNovoRep1V3
GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Il200JunctionsRep1V3
GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2

exons, genedenovo, junctions, splices... which file is more recommended? I guess all are important for different things, but I just want to take a general look

I also have this one:

GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapExonsDeNovo
GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapTranscriptDeNovoV2
GSM765388_hg19_wgEncodeCshlLongRnaSeqMcf7CellPapGeneDeNovoV2
MCF-7_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8686-015WC-b1.LID8687-016WC-b2

Can anyone give a bit of light in this path?

Thanks in advance!
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