annotate mirgene.loc.sample @ 4:fbb1f770ab77 draft

Uploaded
author glogobyte
date Wed, 13 Oct 2021 16:23:59 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
1 # bowtie2_indices.loc.sample
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
2 # This is a *.loc.sample file distributed with Galaxy that enables tools
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
5 # First create these data files and save them in your own data directory structure.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
7 # Copy this file, save it with the same name (minus the .sample),
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
8 # follow the format examples, and store the result in this directory.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
9 # The file should include an one line entry for each index set.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
10 # The path points to the "basename" for the set, not a specific file.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
11 # It has four text columns seperated by TABS.
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
12 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
14 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
15 # So, for example, if you had hg18 indexes stored in:
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
16 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
17 # /depot/data2/galaxy/hg19/bowtie2/
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
18 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
19 # containing hg19 genome and hg19.*.bt2 files, such as:
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
27 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
28 # then the bowtie2_indices.loc entry could look like this:
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
29 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
30 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
31 Hsa Human (Homo sapiens) - hg38
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
32 Mml Rhesus monkey (Macaca mulatta) - rheMac8
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
33 Mmu House mouse (Mus musculus) - mm10
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
34 Rno Norway rat (Rattus norvegicus) - rn6
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
35 Cpo Guinea pig (Cavia porcellus) - cavPor3
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
36 Ocu Rabbit (Oryctolagus cuniculus) - oryCun2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
37 Cfa Dog (Canis familiaris) - canFam3
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
38 Bta Cow (Bos taurus) - bosTau8
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
39 Dno Nine-banded armadillo (Dasypus novemcinctus) - dasNov3
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
40 Ete Lesser hedgehog tenrec (Echinops telfairi) - echTel2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
41 Sha Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
42 Mdo Gray short-tailed opossum (Monodelphis domestica) - monDom5
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
43 Oan Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
44 Gga Chicken (Gallus gallus) - galGal5
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
45 Cli Rock pigeon (Columba livia) - colLiv2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
46 Tgu Zebra finch (Taeniopygia guttata) - taeGut3.2.4
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
47 Ami American alligator (Alligator mississippiensis) - allMis1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
48 Cpi Western painted turtle (Chrysemys picta bellii) - chrPic1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
49 Aca Green anole lizard (Anolis carolinensis) - anoCar2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
50 Xtr Tropical clawed frog (Xenopus tropicalis) - xenTro7
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
51 Dre Zebrafish (Danio rerio) - danRer11
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
52 Sto Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
53 Cin Sea Squirt (Ciona intestinalis) - ci3
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
54 Bfl Florida lancelet (Branchiostoma floridae) - BFL_v2.0
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
55 Sko Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
56 Pfl Ptychodera (Ptychodera flava) - Pfl
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
57 Spu Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
58 Pmi Bat starfish (Patiria miniata) - Pmin1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
59 Dme Fruit fly (Drosophila melanogaster) - dm6
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
60 Dan Fruit fly (Drosophila ananassae) - Dana_caf1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
61 Dmo Fruit fly (Drosophila mojavensis) - Dmoj_caf1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
62 Aae Yellow fever mosquito (Aedes aegypti) - Aaeg_L3
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
63 Hme Longwing butterfly (Heliconius melpomene) - Hmel_1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
64 Tca Red flour beetle (Tribolium castaneum) - Tcas5.2
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
65 Bge Cockroach (Blattella germanica) - Bger_2.0
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
66 Dpu Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
67 Isc Deer tick (Ixodes scapularis) - IscaWI
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
68 Cel Roundworm (Caenorhabditis elegans) - ce11
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
69 Cbr Roundworm (Caenorhabditis briggsae) - CB4
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
70 Asu Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
71 Cte Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
72 Efe Common brandling worm (Eisenia fetida) - Efe_combined
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
73 Lgi Owl limpet (Lottia gigantea) - Lotgi1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
74 Cgi Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
75 Lan Lingula (Lingula anatina) - LinAna_1.0
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
76 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
77 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
78 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
79 #
fbb1f770ab77 Uploaded
glogobyte
parents:
diff changeset
80 #