This script split GBS fastq file by barcode sequences.
Usage: GBS_barcode.pl yourBarCodeFile yourEnzymeFile
You will need to create two text files first, a barcode file and an enzyme file. Barcode File Example (see the example file, tab delimited text file with 4 columns, code p for paired end, you will need to provide the first end file under the file column :
| SampleName | code | paired | file |
|---|---|---|---|
| s1 | CTCC | s | my_1.fastq |
| s2 | TGCA | s | my_1.fastq |
| s3 | ACTA | s | my_1.fastq |
| s4 | GTCT | s | my_1.fastq |
| s5 | GAAT | s | my_1.fastq |
| s6 | GCGT | s | my_1.fastq |
| s7 | TGGC | s | my_1.fastq |
| s8 | CGAT | s | my_1.fastq |
| s9 | CTTGA | s | my_1.fastq |
| s10 | TCACC | s | my_1.fastq |
| s11 | CTAGC | s | my_1.fastq |
| s12 | ACAAA | s | my_1.fastq |
| s13 | TTCTC | s | my_1.fastq |
| s14 | AGCCC | s | my_1.fastq |
Enzyme File Example (ApeKI):
Enzyme: C[AT]GC
FinalSize: 64
Ends: GCTGGATC,GCAGGATC,GCTGAGAT,GCAGAGAT,GCAGC,GCTGC
EnzymeEndSize: 4
Note:
- If you works in Linux or Mac environment, you can use gzip compressed Illumina files directly, as long as the file names end with .gz.
- In barcode file, "s" refere to single end Illumina data, "p" refer to paired end Illumina data. For paired end data files, you only need to provide the first file (with _1 in file name). The second file should have "_2" in file name, and will automatically be recognized.
- In the enzyme file, you are required to provide final size. If reads are shorter than the final size after trimming of the barcode and 3' adapter, the read will be padded with "N" at 3' end.
- Some sample enzyme files are provided here.
Download the PERL script.
- Qi Sun
This project is licensed under the MIT License - see the LICENSE.md file for details