#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_index2.loc #file similar to this one (store it in this directory) that points to #the directories in which those files are stored. The rnastar_index2.loc #file has this format (longer white space characters are TAB characters): # # # #The column should be 1 or 0, indicating whether the index was made #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not, #respecively. # #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 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 dm3 dm3 Fruit Fly (Drosophila melanogaster): dm3 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/dm3/dataset_950794_files 0 dm6 dm6 D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6) /cvmfs/data.galaxyproject.org/managed/rnastar_index2/dm6/dataset_950795_files 0 hg19 hg19 Human (Homo sapiens) (b37): hg19 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/hg19/dataset_950899_files 0 hg38 hg38 Human (Homo sapiens) (b38): hg38 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/hg38/dataset_950901_files 0 mm9 mm9 Mouse (Mus musculus): mm9 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/mm9/dataset_952365_files 0 mm10 mm10 Mouse (Mus Musculus): mm10 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/mm10/dataset_952366_files 0 sacCer2 sacCer2 Yeast (Saccharomyces cerevisiae): sacCer2 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/sacCer2/dataset_952369_files 0 sacCer3 sacCer3 Yeast (Saccharomyces cerevisiae): sacCer3 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/sacCer3/dataset_952370_files 0 ce10 ce10 C. elegans (WS220): ce10 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/ce10/dataset_952371_files 0 ce9 ce9 C. elegans (WS210): ce9 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/ce9/dataset_952372_files 0 rn5 rn5 Rat (Rattus norvegicus): rn5 /cvmfs/data.galaxyproject.org/managed/rnastar_index2/rn5/dataset_952367_files 0 rn6 rn6 Rat Jul. 2014 (RGSC 6.0/rn6) (rn6) /cvmfs/data.galaxyproject.org/managed/rnastar_index2/rn6/dataset_952368_files 0 apiMel4 apiMel4 A. mellifera 04 Nov 2010 (Amel_4.5/apiMel4) (apiMel4) /cvmfs/data.galaxyproject.org/managed/rnastar_index2/apiMel4/dataset_1130463_files 0 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_index2/Amel_4.5/dataset_1130464_files 0