#This is a sample file distributed with Galaxy that enables tools #to use a directory of rna-star indexed sequences data files. #You will need to create these data files and then create a #rnastar_index2x_versioned.loc file similar to this one (store it in this #directory) that points to the directories in which those files are stored. #The rnastar_index2x_versioned.loc file has this format (longer white space #characters are TAB characters): # # # #The column should be 1 or 0, indicating whether the index #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) #or not. # #The column indicates the STAR version that introduced the format of #the index, i.e., the oldest STAR version that could make use of the index. # #Note that STAR indices can become quite large. Consequently, it is only #advisable to create indices with annotations if it's known ahead of time that #(A) the annotations won't be frequently updated and (B) the read lengths used #will also rarely vary. If either of these is not the case, it's advisable to #create indices without annotations and then specify an annotation file and #maximum read length (minus 1) when running STAR. # #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a hg38 hg38 Human (Homo sapiens) (b38): hg38 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/hg38/hg38/dataset_fdfceb86-2b00-45f3-a3f4-63794ea8182d_files 0 2.7.4a hg19 hg19 Human (Homo sapiens) (b37): hg19 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/hg19/hg19/dataset_d34482b9-5123-4ac6-b22d-89a2c5588299_files 0 2.7.4a mm10 mm10 Mouse (Mus Musculus): mm10 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/mm10/mm10/dataset_5e31b655-e1b3-4c90-ae18-bbafb09a15fc_files 0 2.7.4a rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/rn6/rn6/dataset_d0061d40-7013-4497-b3f7-7d57b2a1a38c_files 0 2.7.4a dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm6/dm6/dataset_d5ef3124-4a1d-46a0-886d-9e2e443c840f_files 0 2.7.4a ce10 ce10 C. elegans (WS220): ce10 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/ce10/ce10/dataset_4acc8f48-c175-418c-9ce3-2f47447519f9_files 0 2.7.4a dm3 dm3 Fruit Fly (Drosophila melanogaster): dm3 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/dm3/dm3/dataset_10797bbe-186d-4c6a-b139-e271fd641137_files 0 2.7.4a mm9 mm9 Mouse (Mus musculus): mm9 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/mm9/mm9/dataset_13ca02f1-47ac-4793-969f-103e1ec04c24_files 0 2.7.4a sacCer3 sacCer3 Yeast (Saccharomyces cerevisiae): sacCer3 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/sacCer3/sacCer3/dataset_ee6db620-7c48-4da0-8451-017d274c97ca_files 0 2.7.4a sacCer2 sacCer2 Yeast (Saccharomyces cerevisiae): sacCer2 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/sacCer2/sacCer2/dataset_166fc7cd-9ff8-4acf-9614-a267eeaf9355_files 0 2.7.4a ce9 ce9 C. elegans (WS210): ce9 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/ce9/ce9/dataset_d26ede5d-92f0-481e-af5a-df1b27e7a6fe_files 0 2.7.4a rn5 rn5 Rat (Rattus norvegicus): rn5 /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/rn5/rn5/dataset_ce95c5ad-dcdc-421a-af7f-f5680922d395_files 0 2.7.4a apiMel4 apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/apiMel4/apiMel4/dataset_95aec843-8c04-4d1e-ab44-6888c1fdfefb_files 0 2.7.4a Amel_4.5 Amel_4.5 A. mellifera Nov. 2010 (GCF_000002195.4/Amel_4.5) (Amel_4.5) /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/Amel_4.5/Amel_4.5/dataset_c53a2b2d-8347-4188-82ad-aed87c416f38_files 0 2.7.4a hg19chrX hg19 Human (Homo sapiens) (b37): hg19 chrX /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/hg19/hg19chrX/dataset_7695a11f-c9d6-4ed1-bab3-e195e057f2d4_files 0 2.7.4a