Changes between Version 2 and Version 3 of BIOS_ReferenceFiles


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Timestamp:
Oct 25, 2016 12:23:39 PM (7 years ago)
Author:
rick
Comment:

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  • BIOS_ReferenceFiles

    v2 v3  
    88We use Ensembl as our primary source of annotation and fix it at v.71 ([http://apr2013.archive.ensembl.org/biomart/martview link to archived v.71 BioMart]). To get this version of Ensemble in the R package biomaRt:\\
    99ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "apr2013.archive.ensembl.org", path = "/biomart/martservice" , dataset = "hsapiens_gene_ensembl")
    10 G=getBM(c("chromosome_name", "start_position","end_position","ensembl_gene_id"), mart=ensembl) (currently unavailable..). Reference files are stored here:
    11 /virdir/Scratch/RP3_data/reference/. Locations of genes measured by RNA-seq: /virdir/Scratch/RP3_data/reference/gene_locations_v71.txt
     10G=getBM(c("chromosome_name", "start_position","end_position","ensembl_gene_id"), mart=ensembl) (currently unavailable..). Reference files are stored at the VM here: /virdir/Scratch/RP3_data/reference/. Locations of genes measured by RNA-seq: /virdir/Scratch/RP3_data/reference/gene_locations_v71.txt
    1211
    1312== This table describes the reference and annotation files. ==