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Best Hit for Blat Output

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pslReps - analyse repeats and generate genome wide best
alignments from a sorted set of local alignmentsThis app uses tools that accompany blat, pslReps and pslSort.
It chooses the better alignments from the psl output file from Blat.

Quick Start

• To use Best Hit for Blat Output, import your data in ___ psl format.
• Resources:http https://replaceusers.withsoe.URL.for.tool.documentation.from.the.tool.source.orgucsc.edu/~kent/src/

Test Data

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from neo.psl from the directory above as test input.

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 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

• Use these parameters within the DE app interface:
  • parameter name - value/setting
  • parameter name - value/setting

• Default parameters only, but change the output name for the psl to neo_best.psl.

Output File(s)

Expect a text file named after the input files as psl as output. For the test case, the output file you will find in the example_data directory is named BeautifulProseneo_best.txtpsl.

Tool Source for App

• httphttps://replaceusers.withsoe.URL.for.tool.orgucsc.edu/~kent/src/