Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.
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btrim
Community rating: ?????
Quality trimming of nucleotide sequences (using a sliding window) in a FASTQ file. This version takes a single input file and does quality trimming only (No adapter search).
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- To use btrim, import your data in ___ fastq format.
- Resources: http://replacegraphics.withmed.URL.for.tool.documentation.from.the.tool.source.orgyale.edu/trim/readme
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory. btrim |
Input File(s)
Use TerriblyIncomprehensiblejumpcorr.txt and HorriblyWritten.txt from A.fastq from the directory above as test input.
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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 either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
- Default parameters only, no further configuration needed.
OR
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Select input file: /iplant/home/rogerab/testfiles/jumpcorr.A.fastq
Sliding window size: Integer 5
Quality score: Integer 15
Minimum sequence length: Integer 25
Sanger/Illumina 1.9 (PHRED+33): Flag true
Output File(s)
Expect a text fastq file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txtjumpcorr.A-trimming.fastq.
Tool Source for App
- http://replacegraphics.withmed.URL.for.tool.orgyale.edu/trim/