TPMcalculator¶

Description¶

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. The input parameters are the same GTF files used to generate the alignments, and one or multiple input BAM file(s) containing either single-end or paired-end sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons and introns respectively.

Environment Modules¶

Run module spider tpmcalculator to find out what environment modules are available for this application.

Environment Variables¶

HPC_TPMCALCULATOR_DIR - installation directory
HPC_TPMCALCULATOR_BIN - executable directory

Categories¶

phylogenetics