Entering edit mode
6.4 years ago
lagartija
▴
160
Hi,
I'm trying to extract fast files from fast5 files with poretools with this simple command :
poretools fastq directory_where_fast5files_are/
It seams to work but then I can't find any fast file. Do you know where there end ?
Thank you very much in advance,
Poretools help page says that
How saving that output would work with a directory of files is not clear.
exactly. I tried creating a directory
poretools fastq directory_where_fast5files_are/ > extractedbut it comes back withextracted: Is a directoryit does not work if I create a file neitherPlease select sensible tags, in this case "nanopore" and "poretools" would make sense.
Also, can you elaborate on where you obtained the data and whether it's recently generated? Since quite a while albacore (basecalling software) outputs fastq files directly, essentially making poretools obsolete. I don't think this tool is maintained much too.
What makes you think it's working?
Finally, there is no such a thing as a "fast" file. You either mean fasta, fastq or fast5.
I see, the data is from 2017, that may be why I have fast5files. Sorry for the misspelling. I ment fastq (autocorrect...)
It seams to work because I don't get any error message .
What happens if you use one file as input instead of the whole directory? Does fastq format output get printed to screen?
For reference, the poretools manual on fastq extraction.
Does poretools work on the included
test_datafolder?Do you know which flowcell type and library prep kit was used?
Unless the chemistry is deprecated, I absolutely recommend repeating the basecalling with the latest albacore version to get the most accurate results. That would also solve your fastq output issue.
It might also be that your fast5 files do not contain basecalls.
I think I will do the base calling again with albacore (or deepnano) but I can't find a good documentation. Do you know where I can find more info about this software ?
I advice against using deepnano, see this GitHub repo for an extensive comparison on basecallers. DeepNano is not as accurate as albacore. Do you have access to the nanopore community pages?
Yep I do.
Thank you for your help. I am doing the base calling again with all the "uploads" fast5 files with albacore. I'm not done yet but it also seems much faster that metrichor.