Usage

Usage: ./bin/TPMCalculator -g GTF_file [-d BAM_files_directory|-i BAM_file]

./bin/TPMCalculator options:

    -v    Print info
    -h    Display this usage information.
    -g    GTF file
    -d    Directory with the BAM files
    -b    BAM file
    -k    Gene key to use from GTF file. Default: gene_id
    -t    Transcript key to use from GTF file. Default: transcript_id
    -c    Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the reads length
    -p    Use only properly paired reads. Default: No. Recommended for paired-end reads.
    -q    Minimum MAPQ value to filter out reads. Default: 0. This value depends on the aligner MAPQ value.
    -o    Minimum overlap between a reads and a feature. Default: 8.
    -e    Extended output. This will include transcript level TPM values. Default: No.
    -a    Print out all features with read counts equal to zero. Default: No.