annotate mirbase.loc @ 12:023cbd52a896 draft

Uploaded
author glogobyte
date Wed, 13 Oct 2021 16:14:32 +0000
parents 0e71fc1eaea2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
1 # bowtie2_indices.loc.sample
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
2 # This is a *.loc.sample file distributed with Galaxy that enables tools
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
5 # First create these data files and save them in your own data directory structure.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
7 # Copy this file, save it with the same name (minus the .sample),
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
8 # follow the format examples, and store the result in this directory.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
9 # The file should include an one line entry for each index set.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
10 # The path points to the "basename" for the set, not a specific file.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
11 # It has four text columns seperated by TABS.
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
12 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
14 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
15 # So, for example, if you had hg18 indexes stored in:
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
16 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
17 # /depot/data2/galaxy/hg19/bowtie2/
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
18 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
19 # containing hg19 genome and hg19.*.bt2 files, such as:
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
27 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
28 # then the bowtie2_indices.loc entry could look like this:
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
29 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
30 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
31 hg38 Homo sapiens - GRCh38 hsa.gff3 Homo sapiens
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
32 mm10 Mus musculus - GRCm38 mmu.gff3 Mus musculus
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
33 BosTau5 Bos taurus - Btau_5.0.1 bta.gff3 Bos taurus
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
34 Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana - TAIR10 ath.gff3 Arabidopsis thaliana
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
35 droSim1 Drosophila simulans - dsim_caf1 dsi.gff3 Drosophila simulans
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
36 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
37 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
38 #
0e71fc1eaea2 Uploaded
glogobyte
parents:
diff changeset
39 #