Mercurial > repos > glogobyte > armdb
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author | glogobyte |
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date | Mon, 16 Oct 2023 14:27:15 +0000 |
parents | fbb1f770ab77 |
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# bowtie2_indices.loc.sample # This is a *.loc.sample file distributed with Galaxy that enables tools # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup # First create these data files and save them in your own data directory structure. # Then, create a bowtie_indices.loc file to use those indexes with tools. # Copy this file, save it with the same name (minus the .sample), # follow the format examples, and store the result in this directory. # The file should include an one line entry for each index set. # The path points to the "basename" for the set, not a specific file. # It has four text columns seperated by TABS. # # <unique_build_id> <dbkey> <display_name> <file_base_path> # # So, for example, if you had hg18 indexes stored in: # # /depot/data2/galaxy/hg19/bowtie2/ # # containing hg19 genome and hg19.*.bt2 files, such as: # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # # then the bowtie2_indices.loc entry could look like this: # # Hsa Human (Homo sapiens) - hg38 Mml Rhesus monkey (Macaca mulatta) - rheMac8 Mmu House mouse (Mus musculus) - mm10 Rno Norway rat (Rattus norvegicus) - rn6 Cpo Guinea pig (Cavia porcellus) - cavPor3 Ocu Rabbit (Oryctolagus cuniculus) - oryCun2 Cfa Dog (Canis familiaris) - canFam3 Bta Cow (Bos taurus) - bosTau8 Dno Nine-banded armadillo (Dasypus novemcinctus) - dasNov3 Ete Lesser hedgehog tenrec (Echinops telfairi) - echTel2 Sha Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces Mdo Gray short-tailed opossum (Monodelphis domestica) - monDom5 Oan Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces Gga Chicken (Gallus gallus) - galGal5 Cli Rock pigeon (Columba livia) - colLiv2 Tgu Zebra finch (Taeniopygia guttata) - taeGut3.2.4 Ami American alligator (Alligator mississippiensis) - allMis1 Cpi Western painted turtle (Chrysemys picta bellii) - chrPic1 Aca Green anole lizard (Anolis carolinensis) - anoCar2 Xtr Tropical clawed frog (Xenopus tropicalis) - xenTro7 Dre Zebrafish (Danio rerio) - danRer11 Sto Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome Cin Sea Squirt (Ciona intestinalis) - ci3 Bfl Florida lancelet (Branchiostoma floridae) - BFL_v2.0 Sko Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1 Pfl Ptychodera (Ptychodera flava) - Pfl Spu Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1 Pmi Bat starfish (Patiria miniata) - Pmin1 Dme Fruit fly (Drosophila melanogaster) - dm6 Dan Fruit fly (Drosophila ananassae) - Dana_caf1 Dmo Fruit fly (Drosophila mojavensis) - Dmoj_caf1 Aae Yellow fever mosquito (Aedes aegypti) - Aaeg_L3 Hme Longwing butterfly (Heliconius melpomene) - Hmel_1 Tca Red flour beetle (Tribolium castaneum) - Tcas5.2 Bge Cockroach (Blattella germanica) - Bger_2.0 Dpu Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0 Isc Deer tick (Ixodes scapularis) - IscaWI Cel Roundworm (Caenorhabditis elegans) - ce11 Cbr Roundworm (Caenorhabditis briggsae) - CB4 Asu Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces Cte Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0 Efe Common brandling worm (Eisenia fetida) - Efe_combined Lgi Owl limpet (Lottia gigantea) - Lotgi1 Cgi Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1 Lan Lingula (Lingula anatina) - LinAna_1.0 # # # # #