Mercurial > repos > iuc > data_manager_star_index_builder
annotate tool-data/rnastar_index2_versioned.loc.sample @ 6:54cddd903437 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
| author | iuc |
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| date | Thu, 11 Jul 2019 11:35:38 -0400 |
| parents | |
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| rev | line source |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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2 #to use a directory of rna-star indexed sequences data files. You will |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
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3 #need to create these data files and then create a rnastar_index2.loc |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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4 #file similar to this one (store it in this directory) that points to |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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5 #the directories in which those files are stored. The rnastar_index2.loc |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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6 #file has this format (longer white space characters are TAB characters): |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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7 # |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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9 # |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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changeset
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10 #The <with_gene_model> column should be 1 or 0, indicating whether the index |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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changeset
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11 #was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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12 #or not. |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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13 # |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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14 #The <version> column indicates the STAR version that introduced the format of |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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15 #the index, i.e., the oldest STAR version that could make use of the index. |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
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16 # |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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17 #Note that STAR indices can become quite large. Consequently, it is only |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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18 #advisable to create indices with annotations if it's known ahead of time that |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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19 #(A) the annotations won't be frequently updated and (B) the read lengths used |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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20 #will also rarely vary. If either of these is not the case, it's advisable to |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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21 #create indices without annotations and then specify an annotation file and |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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22 #maximum read length (minus 1) when running STAR. |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
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23 # |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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changeset
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24 #hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
diff
changeset
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25 #hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a |
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54cddd903437
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
iuc
parents:
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