Time stamp from fast5 files

[yk-tanigawa]

objective

• would like to have a plot
  • x-axis time
  • y-axis total length of nucleotides (on chromosome 22)

method

• try to use poretools, porekit, or some other software
• if all of them fails, need to write a script to read fast5 file directly

[yk-tanigawa]

[HDF5 view] FAST5 file has time stamp

[porekit] porekit version 0.1.0 alpha does not work

• dependencies are hard coded in the source code

[poretools]

• works for some of the files, but not all
• Found several people are sending pull request to the main repo.
  • Planning to try some of them
• GitHub repos:
  • main
    • https://github.com/arq5x/poretools
  • other contributors
    • Updates to account for new MinKNOW v1.4 subdirectory structure arq5x/poretools#116
      • https://github.com/tomsasani/poretools
    • Update Fast5File.py arq5x/poretools#104

[yk-tanigawa]

Time_vs_Total_read_length_plot

• notebook is here:
  • https://github.com/rivas-lab/nanopore/blob/a58ca096ea1e05debb3ef8b5a103e7ff7a9d7234/dev/scripts/20170211/20170211_Time_vs_Total_read_length_plot.ipynb

[yk-tanigawa]

Yield plot for chromosome 20 (from all FAST5 files from release 3)

Yield plot for chromosome 20, read length >= 12.5 kb (from all FAST5 files from release 3)

notes are in /dev/scripts/20170219