Mercurial > repos > mvdbeek > bam_readtagger

annotate all_fasta.loc.sample @ 57:38ae00c376ef draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8186814619b9163944e3c11cb797f02c94804ecb
author mvdbeek
date Mon, 29 Jul 2019 10:52:49 -0400
parents 7191da0bc7be
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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1 #This file lists the locations and dbkeys of all the fasta files
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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2 #under the "genome" directory (a directory that contains a directory
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
5 #TAB characters):
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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6 #
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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8 #
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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9 #So, all_fasta.loc could look something like this:
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
10 #
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
14 #
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
17 #such as with hg19 above.
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
18 #