tin.py¶

Calculate the Transcript Integrity Number (TIN) for each transcript in a BED file. TIN is conceptually similar to RIN (RNA Integrity Number) but provides transcript-level measurement of RNA quality and is more sensitive to RNA degradation.

Usage¶

tin.py -i input.bam -r gene_model.bed

Options¶

Option	Description	Default
`-i`, `--input`	Input BAM file(s). Accepts a single BAM, comma-separated BAMs, or a directory of BAM files. All must be sorted and indexed	Required
`-r`, `--refgene`	Reference gene model in BED format (standard 12-column)	Required
`-c`, `--minCov`	Minimum number of reads mapped to a transcript	10
`-n`, `--sample-size`	Number of equally-spaced positions sampled from each mRNA	100
`-s`, `--subtract-background`	Subtract background noise estimated from intronic reads	Off

Output¶

Tab-separated file to stdout with columns: geneID, chrom, tx_start, tx_end, TIN
Summary statistics printed to stderr (median TIN)