Changes between Version 2 and Version 3 of BIOS_ReferenceFiles

Timestamp:

Oct 25, 2016 12:23:39 PM (8 years ago)

Author:

rick

Comment:

--

BIOS_ReferenceFiles

@@ -8 +8 @@
 We 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:\\
 ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "apr2013.archive.ensembl.org", path = "/biomart/martservice" , dataset = "hsapiens_gene_ensembl")
-G=getBM(c("chromosome_name", "start_position","end_position","ensembl_gene_id"), mart=ensembl) (currently unavailable..). Reference files are stored here: 
-/virdir/Scratch/RP3_data/reference/. Locations of genes measured by RNA-seq: /virdir/Scratch/RP3_data/reference/gene_locations_v71.txt
+G=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
 
 == This table describes the reference and annotation files. ==