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FPKM-UQ.py

Calculate count, FPKM, and FPKM-UQ (upper quartile normalized FPKM) values per gene, following the GDC mRNA pipeline definition.

Usage

FPKM-UQ.py --bam input.bam --gtf genes.gtf -o output_prefix

Options

Option Description Default
--bam Alignment file in BAM format (sorted, indexed) Required
--gtf Gene model in GTF format Required
--info Gene model information file 5
-o, --output Prefix of output file Required
--log2 Convert FPKM and FPKM-UQ to log2(x+1) scale Off

Output

Tab-separated file with count, FPKM, and FPKM-UQ values per gene.