Mercurial > repos > glogobyte > isoread
comparison mirgene.loc @ 8:de8a08bd4593 draft
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| author | glogobyte |
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| date | Wed, 13 Oct 2021 16:06:27 +0000 |
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| 7:0e71fc1eaea2 | 8:de8a08bd4593 |
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| 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 # |