corrected sequence not generated

[zhuzhuo]

Hi Tamas,
I'm trying to use PoreSeq to perform error correction without reference, but I got an empty fasta file after the 'poreseq consensus' step, no error was reported in the log file. I didn't exactly follow the instructions, for I couldn't get fasta sequence in the extraction step, which I suspect was due to the hard-coded file path. I got my allreads.fasta by converting fastq to fasta, and I skipped the split step. I have no problem in the alignment step, and I checked the bam file and it looks fine. I wonder what caused the empty corrected fasta file. Your help will be highly appreciated.
Thanks,
Zhu

[tszalay]

Hi Zhu,

I'm not sure what the problem is based on the information you've given me, but more importantly, it's been long enough since I've used or updated these tools that I can't really say they're well supported (as you can tell from the last commits being >2 years ago). You might be better off trying one of the tools suggested in Jared's post (they also deprecated the same part of their pipeline). Overall you will probably have better luck running with nanopolish, as it seems like they've been keeping it up to date.
Sorry I can't be of more help - I no longer work in the nanopore field and nobody has taken over this project.

Best,
Tamas

[zhuzhuo]

Hi Tamas,

Thanks for the reply. I absolutely understand, but I have 2 quick questions if you don't mind... Is there an example dataset to work with? And what is the expected output for the error correction step (poreseq consensus)? Does it correct each and every read?

Thank you for your time,
Zhu

[tszalay]

Hi Zhu,

The expected output is that it corrects every read, yes. I'm not sure where to find an example dataset anymore, it's been a number of years. Much of my testing was on the initial E. coli dataset uploaded by Quick et al. But again, I would expect using more recent tools for the consensus sequence building to be probably 100x faster than using poreseq consensus, so if you have that option I highly recommend it.

Best,
Tamas

[zhuzhuo]

Thanks for the help, Tamas! I'll try some more recent tools.

-Zhu