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GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

Mermasker

Community rating: ?????

Mask fasta sequences on the basis of k-mer occurance frequency identified using Tallymer-search. Output is a hard-masked fasta file and a GFF file describing masked-regions.

Quick Start

Note you must first run Tallymer-search on a set of sequences before you can run Mermasker
To use Mermasker, specify the same fasta file that you used for Tallymer-search. Also specify the Tallymer-search output file "tallymer_search_out.txt"

Resources:

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Tallymer.

Input File(s)

Specify the fasta file used as input for Tallymer-search, in this case "maize_AC145224.fa".

Also specify the output of Tallymer-search "tallymer_search_out.txt".

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use these parameters within the DE app interface:
- k-mer count threshold: Enter the minimum frequency count of the k-mer to be masked. Note that the minimum is limited by the minimum occurrence threshold that was set when using tallymer-mkindex.

Output File(s)

Expect two files. One is a hard-masked sequence file and the other is a GFF. For example:

maize_2BACS.mermask.fasta
maize_2BACS.mermask.gff

Tool Source for App

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Output is a hard-masked fasta file and a GFF file describing masked-regions.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Note you must first run Tallymer-search on a set of sequences before you can run Mermasker","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To use ","type":"text"},{"text":"Mermasker","type":"text","marks":[{"type":"strong"}]},{"text":", specify the same fasta file that you used for Tallymer-search. Also specify the Tallymer-search output file \"tallymer_search_out.txt\"","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Resources:","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://genometools.org/","type":"text","marks":[{"type":"link","attrs":{"href":"http://genometools.org/"}}]}]}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Test data for this app appears directly in the Discovery Environment in the Data window under ","type":"text"},{"text":"Community Data -> iplantcollaborative -> example_data ->","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"Tallymer","type":"text","marks":[{"type":"em"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":".","type":"text"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Specify the fasta file used as input for Tallymer-search, in this case \"maize_AC145224.fa\".","type":"text"}]},{"type":"paragraph","content":[{"text":"Also specify the output of Tallymer-search \"tallymer_search_out.txt\".","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"paragraph","content":[{"text":"When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Use these parameters within the DE app interface:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"k-mer count threshold: Enter the minimum frequency count of the k-mer to be masked. Note that the minimum is limited by the minimum occurrence threshold that was set when using tallymer-mkindex.","type":"text"}]}]}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Expect two files. One is a hard-masked sequence file and the other is a GFF. For example:","type":"text"}]},{"type":"paragraph","content":[{"text":"maize_2BACS.mermask.fasta","type":"text"},{"type":"hardBreak"},{"text":" maize_2BACS.mermask.gff","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Tool Source for App","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://genometools.org/","type":"text","marks":[{"type":"link","attrs":{"href":"http://genometools.org/"}}]}]}]}]}]}]}]}]}],"version":1}}}}]}],"version":1}

Mermasker (archived)

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