Changes between Version 1 and Version 2 of BIOS_ReferenceFiles


Ignore:
Timestamp:
Oct 25, 2016 12:19:19 PM (8 years ago)
Author:
rick
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • BIOS_ReferenceFiles

    v1 v2  
    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)
     10G=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
    1112
    1213== This table describes the reference and annotation files. ==