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TPM calculator 0.0.3

TPM calculator 0.0.3

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.

Quick Start

  • To use TPM calculator 0.0.3, import a GTF file of reference gene annotations and one or more BAM files of mapped sequence data

  • Resources: https://github.com/ncbi/TPMCalculator

Test Data

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

Input Files

Use:

  • reference.gtf

  • bam_files (folder)

Parameters

There are no required parameters.

 

Output Files

This analysis should generate three output files for each input:

  • sample1_genes.ent

  • sample1_genes.out

  • sample1_genes.uni

  • sample2_genes.ent

  • sample2_genes.out

  • sample2_genes.uni

Tool Source for App

https://github.com/ncbi/TPMCalculator