BarcodeParse

Parsing the barcode sequences in CRISPR-Case9 system using Next-generation sequencing

required environment

1. Python => 3.6
2. pandas
3. numpy

Schematic diagram

paraments:

1. -R1 R1 fastq sequence file (gizped or uncompressed)
2. -R2 R2 fastq sequence file (gizped or uncompressed)
3. -vector5 vector sequence adjacent to 5' barcode (default='TATAAGCGAAAGAAGCATCAGATGGGCAAACAAAGCACCAGTGGTCTAGTGGTAGAATAGTACCCTGCCACGGTACAGACCCGGGTTCGATTCCCGGCTGGTGCA')
4. -vector3 vector sequence adjacent to 3' barcode (default='TAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTTTTAGCGCGTGCATGCCTGCAGGTCCACAAATTCGGGTC')
5. -o out put file

    python barcode_parser.py -h 

usage: barcode_parser.py [-h] [-R1 R1] [-R2 R2] [-verctor5 VERCTOR5]
                         [-verctor3 VERCTOR3] [-o O]

optional arguments:
  -h, --help          show this help message and exit
  -R1 R1              R1 sequence file
  -R2 R2              R2 sequence file
  -vector5 VERCTOR5  verctor sequence adjacent to 5' barcode
  -verctor3 VERCTOR3  verctor sequence adjacent to 3' barcode
  -o O                out put file

header of output

1. barcodeID unique barcode id
2. barcodesequence barcode sequence
3. barcodeCount the number of barcode sequence been sequenced
4. sgRNAsequence sgRNA sequence
5. sgRNACount the number of sgRNA sequence been sequenced

 #example 
 python barcode_parser.py -R1 testData/test_R1.fastq -R2 testData/test_R2.fastq -vector5 GCGAAAGAAGCATCAGATGGGCAAACAAAGCACCAGTGGTCTAGTGGTAGAATAGTACCCTGCCACGGTACAGACCCGGGTTCGATTCCCGGCTGGTGCA -vector3 GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTTTTAGCGCGTGCATGCCTGCAGGTCCACAAATTCGGGTC -o testData/sgRNA_count.txt