comparison mirgene.loc.sample @ 15:37aaa551e5fd draft

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author glogobyte
date Wed, 13 Oct 2021 16:16:12 +0000
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14:5a717167284f 15:37aaa551e5fd
1 # bowtie2_indices.loc.sample
2 # This is a *.loc.sample file distributed with Galaxy that enables tools
3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
5 # First create these data files and save them in your own data directory structure.
6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
7 # Copy this file, save it with the same name (minus the .sample),
8 # follow the format examples, and store the result in this directory.
9 # The file should include an one line entry for each index set.
10 # The path points to the "basename" for the set, not a specific file.
11 # It has four text columns seperated by TABS.
12 #
13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
14 #
15 # So, for example, if you had hg18 indexes stored in:
16 #
17 # /depot/data2/galaxy/hg19/bowtie2/
18 #
19 # containing hg19 genome and hg19.*.bt2 files, such as:
20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
27 #
28 # then the bowtie2_indices.loc entry could look like this:
29 #
30 #
31 Hsa Human (Homo sapiens) - hg38
32 Mml Rhesus monkey (Macaca mulatta) - rheMac8
33 Mmu House mouse (Mus musculus) - mm10
34 Rno Norway rat (Rattus norvegicus) - rn6
35 Cpo Guinea pig (Cavia porcellus) - cavPor3
36 Ocu Rabbit (Oryctolagus cuniculus) - oryCun2
37 Cfa Dog (Canis familiaris) - canFam3
38 Bta Cow (Bos taurus) - bosTau8
39 Dno Nine-banded armadillo (Dasypus novemcinctus) - dasNov3
40 Ete Lesser hedgehog tenrec (Echinops telfairi) - echTel2
41 Sha Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces
42 Mdo Gray short-tailed opossum (Monodelphis domestica) - monDom5
43 Oan Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces
44 Gga Chicken (Gallus gallus) - galGal5
45 Cli Rock pigeon (Columba livia) - colLiv2
46 Tgu Zebra finch (Taeniopygia guttata) - taeGut3.2.4
47 Ami American alligator (Alligator mississippiensis) - allMis1
48 Cpi Western painted turtle (Chrysemys picta bellii) - chrPic1
49 Aca Green anole lizard (Anolis carolinensis) - anoCar2
50 Xtr Tropical clawed frog (Xenopus tropicalis) - xenTro7
51 Dre Zebrafish (Danio rerio) - danRer11
52 Sto Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome
53 Cin Sea Squirt (Ciona intestinalis) - ci3
54 Bfl Florida lancelet (Branchiostoma floridae) - BFL_v2.0
55 Sko Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1
56 Pfl Ptychodera (Ptychodera flava) - Pfl
57 Spu Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1
58 Pmi Bat starfish (Patiria miniata) - Pmin1
59 Dme Fruit fly (Drosophila melanogaster) - dm6
60 Dan Fruit fly (Drosophila ananassae) - Dana_caf1
61 Dmo Fruit fly (Drosophila mojavensis) - Dmoj_caf1
62 Aae Yellow fever mosquito (Aedes aegypti) - Aaeg_L3
63 Hme Longwing butterfly (Heliconius melpomene) - Hmel_1
64 Tca Red flour beetle (Tribolium castaneum) - Tcas5.2
65 Bge Cockroach (Blattella germanica) - Bger_2.0
66 Dpu Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0
67 Isc Deer tick (Ixodes scapularis) - IscaWI
68 Cel Roundworm (Caenorhabditis elegans) - ce11
69 Cbr Roundworm (Caenorhabditis briggsae) - CB4
70 Asu Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces
71 Cte Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0
72 Efe Common brandling worm (Eisenia fetida) - Efe_combined
73 Lgi Owl limpet (Lottia gigantea) - Lotgi1
74 Cgi Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1
75 Lan Lingula (Lingula anatina) - LinAna_1.0
76 #
77 #
78 #
79 #
80 #