positions for barcodes do not work at all!

[antonkulaga]

The version in pip does not seem to work at all! I manually checked barcodes and they exist, but I get everything UNKNOWN for:

demultiplex demux -r -s 3 -e 9 barcodes.txt S3987Nr1.1.fastq S3987Nr1.2.fastq 

barcodes.txt

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S3987Nr1.2_sample4-n10000.fastq.txt
S3987Nr1.1_sample4-n10000.fastq.txt…]()

[jfjlaros]

It seems your barcodes are of length 9 and have wildcards (Ns) in them, yet you select seven nucleotides from the read.

Perhaps you can try to remove the three Ns from your barcodes and select six nucelotides from the read (e.g., -s 4 -e 9).