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tszalay / poreseq

Error correction and variant calling algorithm for nanopore sequencing
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poreseq does not extract 2D fasta sequences #9

Open jazberna1 opened 5 years ago

jazberna1 commented 5 years ago

Hello,

I'm running 'poreseq extract' to get the sequence out a folder containing the fast5 files. I get no sequences extracted getting the message 'Done, extracted 0 2D fasta sequences'. I have checked that fast5 files contain the fastq slot.

I was wondering if there is any obvious mistake I am doing that you can tell me.

Thanks a lot Jorge

tszalay commented 5 years ago

Hi Jorge,

I'm afraid I can't really help you, I haven't maintained this code (I no longer work in the field) and it's likely that something in the output formats have changed. You might want to try one of the alternative nanopore error correction codes.

Best, Tamas

jazberna1 commented 5 years ago

Hi Tamas,

Thanks so much for letting me know.

Jorge