Demutiplex of illumina sequencin

1. Usage of bcl2fastq

bcl2fastq  -R /mnt/hwt2_data2/Hiseq_1000_fio/181127_SNL144_0351_AHMMJGBCX2/ --output-dir ./fastq  --use-bases-mask Y100n,I6n,Y100n  --ignore-missing-bcls --ignore-missing-filter --sample-sheet ./SampleSheet.csv

Explanation of key parameters:
--use-bases-mask Y100n,I6n,Y100n
--use-bases-mask read1,index,read2
"n" represent the base to be skipped.

2. SampleSheet.csv

[Header]
IEMFileVersion,4
Investigator_Name,XX_Lab
Experiment_Name,test
Date,12/04/2018
Workflow,GenerateFASTQ
Application,Hiseq1000_FASTQ_Only
Assay,TruSeq_LT
Description
Chemistry,Default

[Reads]
101
101

[Settings]

[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
1,sample1,,,,,ACAGTG,,
1,sample2,,,,,GCCAAT,,
2,sample3,,,,,GATCAG,,
2,sample4,,,,,TAGCTT,,

3. fastq file

Placed in fastq/ directory.

4. Report

check the report

firefox fastq/Reports/html/index.html

Example: