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Old 11-06-2018, 06:54 AM   #1
igwill
Junior Member
 
Location: usa

Join Date: Nov 2018
Posts: 3
Default Two sets of .fast5 files from Nanopore

Hi,

I am trying to Nanopolish a draft Nanopore genome I assembled with Canu.
For my indexing step, I have two folders in the data given to me by the sequencing service that contain fast5 files.
Which is the correct to use for indexing Nanopolish?

I have one set, in a folder called fast5, which contains folders 0 to 215, each containing fast5 files that are small (20 kb to 1000 kb).

I have a second set, in another folder albacore-2.2.5-FLO-PRO001-SQK-LSK109-by_dir, which contains folders 1 -215, each containing:
configuration.cfg
pipeline.log
sequencing_summary.txt
sequencing_telemetry.js
workspace/
which contains:
fastq_runid_*.fastq
0/
containing fast5 files that are larger (33kb to 10,000 kb)

The names of the files in fast5/1 or albacore*by_dir/1/workspace/0 are exactly the same but differ in size.

I'm leaning toward the larger files as their folder shares a dir with the sequencing_summary.txt. But I'm really not sure. Anyone see this before?

Thank you
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