Hi Julie,

I am hoping to clarify the input to use for the 'binReads.sh' script for binning barcodes. I have GUIDEseq fastq files for 4 samples after demultiplexing in the folder 'fastq' as:

treatment1.i1.fastq treatment1.i2.fastq treatment1.r1.fastq treatment1.r2.fastq treatment1Rep1.i1.fastq treatment1Rep1.i2.fastq treatment1Rep1.r1.fastq treatment1Rep1.r2.fastq treatment1Rep2.i1.fastq treatment1Rep2.i2.fastq treatment1Rep2.r1.fastq treatment1Rep2.r2.fastq control.i1.fastq control.i2.fastq control.r1.fastq control.r2.fastq controlRep1.i1.fastq controlRep1.i2.fastq controlRep1.r1.fastq controlRep1.r2.fastq controlRep2.i1.fastq controlRep2.i2.fastq controlRep2.r1.fastq controlRep2.r2.fastq undetermined.i1.fastq undetermined.i2.fastq undetermined.r1.fastq undetermined.r2.fastq

sh binReads.sh ./fastq GUIDEseq/barcodes 1 8 16 p7.index p5.index usedBarcodes

The outputs are empty fastq files (ex: TAAGGCGATAGATCGC_treatment.*.fastq) and the usedBarcodes file that has a single line:

wc -w usedBarcodes 32 usedBarcodes

Can you please let me know if I am providing the fastq files incorrectly or missing something else?

Thanks Sharvari