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rrwick / Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads
GNU General Public License v3.0
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Albacore + Porechop VS Guppy + Deepbinner #25

Open Jaoquien opened 5 years ago

Jaoquien commented 5 years ago

Hi everyone,

Until recently we used to apply Porechop after Albacore basecalling+demultiplexing. Now, we are using Guppy to basecall and we decided to apply Deepbinner to demultiplex.

My main question is:

If we use Guppy also to demultiplex by barcode, which files should I give as an Input for Deepbinner? Because, while Porechop asks for a file directory, Deepbinner demands a .fastq file. Should I concatenate all .fastq (for example the desired barcode and the unclassified, both pass and fail) files to ensure that I retrieve the maximum number of reads? or what?

Thank you so much,

Quim

mbhall88 commented 5 years ago

If you are wanting to do the same type of filtering as with Albacore + Porechop (i.e only keep reads where both programs agree) you will have to run deepbinner on each barcode directory from guppy.

Additionally, deepbinner only takes one fastq file so you will have to combine all the fastqs in a barcode bin.

Jaoquien commented 5 years ago

@mbhall88 thank you so much for your help