Count linked-read barcodes

You might want a table of the counts (frequency) of all the unique barcodes in your data and that's what count is for. Records with missing barcodes are ignored.

FASTQ

You can use one file of a pair (e.g. R1 or R2), but including both files will prioritize counting the first file and only count occurences of new barcodes in the second file that aren't present in the first file. This is done to avoid double-counting barcodes.

djinn fastq count INPUT...

djinn fastq count sample1.F.fq.gz sample1.R.fq.gz > sample1.bxcount

SAM

Similarly, counting barcodes in SAM/BAM files avoids double-counting by counting forward reads if they are unpaired or unpaired, and reverse reads if they are unpaired or the barcode has not been observed yet.

djinn sam extract INPUT

djinn sam count sample1.bam > sample1.bxcount