Bam to Counts (general)
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Enter a bam file and a matching annotation file and get counts for transcripts or genes
App Creator
Roger Barthelson
Quick Start
- To use Bam to Counts (general), import your data in BAM format, and a GFF file that matches the genome sequence used for the mapping step that created the BAM.
- Resources: http://www.iplantcollaborativecyverse.org/learning-center/discovery-environment/dec-003count-characterizingrna-differentialseq-expressionreads-rnamap-seqtranscripts
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bam2countsGeneral |
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- Default parameters and set feature to count to gene_name.
Output File(s)
Expect a tab-delimited file as output. For the test case, the output file you will find in the example_data directory is named hy5testout.
Tool Source for App
- http://www.iplantcollaborativecyverse.org/learning-center/discovery-environment/dec-003count-characterizingrna-differentialseq-expressionreads-rnamap-seqtranscripts