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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.
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3 #You will need to create these data files and then create a
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4 #rnastar_index2x_versioned.loc file similar to this one (store it in this
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5 directory) that points to the directories in which those files are stored.
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6 #The rnastar_index2x_versioned.loc file has this format (longer white space
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7 #characters are TAB characters):
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8 #
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9 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version>
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10 #
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11 #The <with_gene_model> column should be 1 or 0, indicating whether the index
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12 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
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13 #or not.
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14 #
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15 #The <version> column indicates the STAR version that introduced the format of
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16 #the index, i.e., the oldest STAR version that could make use of the index.
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17 #
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18 #Note that STAR indices can become quite large. Consequently, it is only
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19 #advisable to create indices with annotations if it's known ahead of time that
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20 #(A) the annotations won't be frequently updated and (B) the read lengths used
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21 #will also rarely vary. If either of these is not the case, it's advisable to
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22 #create indices without annotations and then specify an annotation file and
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23 #maximum read length (minus 1) when running STAR.
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24 #
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25 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a
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26 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a
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