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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Heterozygote Bam to Counts
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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
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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.
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 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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