Mercurial > repos > rnateam > sortmerna

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

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