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1 #This is a sample file distributed with Galaxy that enables tools
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2 #to use a directory of rna-star indexed sequences data files. You will
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3 #need to create these data files and then create a rnastar_index2.loc
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4 #file similar to this one (store it in this directory) that points to
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5 #the directories in which those files are stored. The rnastar_index2.loc
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6 #file has this format (longer white space characters are TAB characters):
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7 #
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <withGTF>
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9 #
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10 #The <with_gtf> column should be 1 or 0, indicating whether the index was made
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11 #with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
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12 #respecively.
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13 #
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14 #Note that STAR indices can become quite large. Consequently, it is only
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15 #advisable to create indices with annotations if it's known ahead of time that
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16 #(A) the annotations won't be frequently updated and (B) the read lengths used
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17 #will also rarely vary. If either of these is not the case, it's advisable to
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18 #create indices without annotations and then specify an annotation file and
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19 #maximum read length (minus 1) when running STAR.
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20 #
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21 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0
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22 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
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