3 months ago by
It may be that your files don't have the type of reads that
best extracts. Have you tried using some of the other types, for example
2D, or no type at all? If that outputs something, it's likely that your file doesn't have any reads that match the type
best, which doesn't seem to make much sense -- the poretools documentation seems to imply that something should be output when using
A type of “best” will extract the 2D read, if it exists. If not, it will extract either the template or complement read, whichever is available and has a better average Phred score.
Also keep in mind that the fasta file will be output to stdout; if you'd like them in a file, you'll have to redirect the output.