correctedBed2AllInfo: Make a "corrected" version of the All-Info file after using...

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Make a "corrected" version of the All-Info file after using IsoQuant to identify incorrect splice sites

Description

This function takes in a corrected bed file that is generated after running IsoQuant, as well as the AllInfo file that is the output of scisorseqr. It produces a new AllInfo file with extra columns containing the original and corrected exon and intron chains. Best use case is for Oxford Nanopore data which can have errors in splice-site assignment

Usage

correctedBed2AllInfo(bedPath='Sample_sorted.corrected_reads.bed',
allInfo = "LongReadInfo/AllInfo_IncompleteReads_corrected.gz",
outFile = "LongReadInfo/AllInfo_IncompleteReads_corrected.gz")

Arguments

bedPath	Path to corrected bed file. Currently does not support bed.gz
Path	to the output.gz file. Defaults to the LongReadInfo folder and generates a file named "AllInfo_IncompleteReads_corrected.gz".

Value

A file in the AllInfo_Incomplete format with column 6 being the corrected intron chain, column 9 being the corrected exon chain, and additional columns 10 and 11 being the original intron and exon chains respectively

See Also

InfoPerLongRead

https://github.com/ablab/IsoQuant

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.