Mercurial > repos > yhoogstrate > featurecounts_valid_gff
changeset 33:f9574179f7ea
Uploaded
| author | yhoogstrate |
|---|---|
| date | Fri, 07 Feb 2014 11:28:24 -0500 |
| parents | a6665369ff4f |
| children | 21be93127c42 |
| files | gene_sets.loc.sample |
| diffstat | 1 files changed, 34 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene_sets.loc.sample Fri Feb 07 11:28:24 2014 -0500 @@ -0,0 +1,34 @@ +# Because of this file, galaxy tools can access gene annotations +# provided as GFF / GTF files by selecting on: +# - Priorty (order in the file) +# - Provider +# - dbkey (reference genome id) +# +# The gene_sets.loc file syntax is: +# <name/UID> <dbkey> <path> <provider> <URL/reference*> +# +# *optional +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# + + + +# [UCSC - UCSC Genes: knownGene] + +#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ +#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ + + + +# [RefSeq Genes: RefGene] +# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ + + + +# [ Ensembl] +# link: http://www.ensembl.org/info/data/ftp/index.html + +#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz +#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz