IDseq_split_reads: Split reads from FASTQ files into UMI, antibody barcode and...

In jessievb/IDseq: Split barcoded FASTQ files and analyse data from the IDseq method

Description

First, the IDseq_split_reads function uses shortread package function "readFastq" to load all reads from a .fastq or .fastq.gz file. The fastq files can be zipped (fastq.gz), if doesn't work have a look at if there is a change in the shortread package and file extensions that can be used. Then the reads containing an anchor sequence are extracted and these reads are split to retrieve - UMI - Barcode_1 - Barcode_2 sequences (and stored in a table with 3 columns) Finally a column with the sequencing_ID (folder name that contained the fastq file) is added.

Usage

IDseq_split_reads(fastq_file, matching_distance = 2)

Arguments

fastq_file

fastq formatted files in a directory path. Default settings from ShortRead::readFastq

Value

Saves a .tsv file with four columns: UMI , Barcode_1 , Barcode_2, sample_ID. Location of file: workingdir/output/data/

See Also

for -importing reads from fastq- information ShortRead::readFastq

Examples

IDseq_split_reads("experiment/data/seq_id/sample-ID.fastq.gz", matching_distance = 2) 

jessievb/IDseq documentation built on July 5, 2021, 9:04 p.m.