stLFR_read_demux
This repo provides tools for splitting sequencing read data for stLFR (single-tube LFR) by barcodes.
Input file: Single-end sequencing read fastq file with barcode sequence appended at the end of each sequence. Or Pair-end sequencing read fastq files with barcode sequence appended at the end of read2.
Barcode structure: Each combinatory barcode is consisted of 3 10-base barcode sequence and 2 link sequences.
- 54 base barcode: 10+6+10+18+10
- 42 base barcode: 10+6+10+6+10
Output files: single-end: split_read.fq.gz Pair-end: split_read.1.fq.gz, split_read.2.fq.gz
In the output fastq files, reads are split by barcodes, as indicated in read names after '#' sign, in the format of [0-9]+[0-9]+[0-9]+, each number representing one barcode ID.
To run:
Example: PE100 with 54 base barcodes:
perl split_barcode_PEXXX_54_reads.1.pl barcode.list barcode_RC.list read_1.fq.gz read_2.fq.gz 100 split_read
perl split_barcode_PEXXX_54_reads.2.pl barcode.list barcode_RC.list read_1.fq.gz read_2.fq.gz 100 split_read
Example: SE50 with 42 base barcodes:
perl split_barcode_SEXXX_42RC_reads.1.pl barcode.list barcode_RC.list read1.fq.gz 50 split_read