The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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snp_ase

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Snp_ase  computes a measure of allele-specific expression for NGS read sets by counting ref and alt variants over each locus of a variant set.

Inputs:

1) Directory of bam alignment files

2) Variant file in .vcf format

Outputs:

The program outputs one table for each input .bam file. The tables have a .bed format, as follows:

chrN  123654 123654 28:6:g:a

The first three fields are: chromosome, variant position, variant position (same)

The last field gives the counts of reads at that location having the ref and alt variants:

ref count : alt count: ref base: alt base

The output files are placed in a subdirectory named "Results, and they are named using

the .bam file names with the extension changed to .bed.

A summary table "total_counts.html" is also generated, which shows the total ref/alt counts for

each .bam file, and the ref/alt ratio ("allele bias")

Quick Start

  • Upload your .bam files into one directory under your Discovery Environment space.
  • Upload your variant file (.vcf) to the DE
  • Open the app and browse to these locations
  • Start the analysis

Test Data

Icon

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

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt 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

Output File(s)

Expect a text 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.txt.

Tool Source for App

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