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Heterozygote Bam to Counts, v1.2

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Enter a bam file and a matching annotation file and get counts for transcripts or genes

Quick Start

  • To

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  • use Bam to Counts, v1.2

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  •  import your data in

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  • BAM format, and a GFF file that matches the genome sequence used for the mapping step that created the BAM.
  • Resources: http://

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Test data for

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this app

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 appears directly in the Discovery Environment in the Data window

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under Community Data -> iplantcollaborative -> example_data ->

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bam2countsGeneral

Input File(s)

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Use hy5_rep1.bam and annotation.gff from the directory above as test input.

Parameters Used

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in App

When

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the app

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 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.

 

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  • Default parameters

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  • Default parameters only, no further configuration needed.

OR

  • Use these parameters within the DE app interface:
    • parameter name - value/setting
    • parameter name - value/setting
  • and set feature to count to gene_name.


Output File(s)

Expect

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tab-delimited file as output. For the test case, the output file you will find in the example_data directory is

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named hy5testout.

Tool

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 Source for App

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