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  • 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

  • #2
    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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