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rivas-lab
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nanopore
Tools for analysis of long-read sequencing data.
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Time stamp from fast5 files
#22
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yk-tanigawa
opened
7 years ago
yk-tanigawa
commented
7 years ago
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
commented
7 years ago
[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
https://github.com/arq5x/poretools/pull/116
https://github.com/tomsasani/poretools
https://github.com/arq5x/poretools/pull/104
yk-tanigawa
commented
7 years ago
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
commented
7 years ago
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
objective
method
fast5
file directly