Demultiplexing - barcode bins

[mzakram219]

Dear, I am new to nanopore community and have some questions. I might sound silly!
We preapred nanopore librariy using 1-24 SQK-16S024 kit for 24 samples. After sequencing, i got fastq files, they were subjected to Porechop for demultiplexing and adapter trimming. However, as a output, porechop created only 2 barcode bins, BC01 and BC02. BC01 is a very big file with more than 1 million reads. The question is how many barcode bins were expected after porechop process? I was expecting barcode bins as i used 24 samples for the library preparation. COuld you please share your experience, it might be helpful.
Thanks!

[SebastianDall]

Hi @mzakram219 I am no expert, but have you tried to increase the --check_reads (default: 10.000). It might be that all barcodes are not detected from the initial 10.000 reads checked.

Best, Sebastian

[mzakram219]

Hi @SebastianDall Thank you for your suggestion. I gave it a try and increased the --check reads, and now Porechop is able to make barcode bins for all the samples. Thank you

[SebastianDall]

Fantastic! Will you mark the issue as closed :)