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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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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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a 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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