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

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


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:
which contains:
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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Old 04-07-2019, 04:07 PM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

As far as I'm aware, it doesn't matter. Nanopolish uses the called fastq files together with the signal in the fast5 files, so both should work. I expect the main difference between the two fast5 file types is that one will include the called sequences as an additional folder within the fast5 files.
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