Mercurial > repos > rnateam > sortmerna

comparison tool-data/rRNA_databases.loc.sample @ 3:42509ccf8f59 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Tue, 04 Aug 2015 15:14:58 -0400
parents
children e6727cef3083
comparison
equal deleted inserted replaced
2:6f23678fc6e9 3:42509ccf8f59
1 #This is a sample file distributed with Galaxy that is used to define a
2 #list of public ribosomal databases for SortMeRNA, using the following format
3 #(white space characters are TAB characters):
4 #
5 #<unique_id> <database_caption> <fasta_file_path>
6 #
7 #So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA
8 #file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc
9 #entry would look like this:
10 #
11 #rfam-5.8s-id98 Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s-id98.fasta
12 #
13 #For each rRNA database, you need to create the index files using the
14 #indexdb_rna program provided by SortMeRNA. You need to specify as index
15 #basename the path of the FASTA file without extension. For example, for the
16 #previous database the command is:
17 #
18 # indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98
19 #
20 #Since SortMeRNA comes bundled with eight ribosomal databases, you can use them
21 #by creating the actual index files as explained above and uncommenting the
22 #following lines.
23 #rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta
24 #rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta
25 #silva-arc-16s-id95 SILVA v.119 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta
26 #silva-arc-23s-id98 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta
27 #silva-bac-16s-id90 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta
28 #silva-bac-23s-id98 SILVA v.119 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta
29 #silva-euk-18s-id95 SILVA v.119 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta
30 #silva-euk-28s-id98 SILVA v.119 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta