search

arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
242 stars 90 forks source link

not retrieving data from skip folder #141

Closed jordur closed 7 years ago

jordur commented 7 years ago

Hi all, I used poretools to extract fastq sequences from fast5 PASS files with no problem. However, I was unable to extract valid sequences from files archived on the SKIP folder. i.e

$ poretools stats pass_read.fast5 
total reads 1
total base pairs    1864
mean    1864.00
median  1864
min 1864
max 1864
N25 1864
N50 1864
N75 1864

$ poretools stats skip_read.fast5 
WARNING:poretools:No valid sequences observed.

I have plenty of files in the skip folder (I suspect due to computer resources) and I would like to obtain as much information as possible from the sequencing process. Attached you will find both files. Any advice will be appreciated pass_read.zip skip_read.zip

jordur commented 7 years ago

Damn of me! Sorry for the inconvenience: --group 1 Shame on me... ;) Thank you for your tool!