junction_count

collect the splice junction in an isoform sequence

Usage

junction_count(isoform, count = 1, polyA = 0, sep = ",", split = "|")

Arguments

isoform

The isoform sequence, should be formatted as "s1,e1|s2,e2|...", s means the start site of an exon while e means the end site.

count

The count for each base

polyA

A flag to indicate if the read has a polyA tail

sep

The character to split the start and end sites of an exon.

split

The character to split the exon in the isoform sequence.

Value

A matrix recording the junction count, the first column is the junction identity and the second column is the count