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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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Meaning of cent_signals #16

Closed cednotsed closed 4 years ago

cednotsed commented 5 years ago

Hi,

May I ask what does cent_signal mean exactly?

Also, with reference to your extract features module, how was the signal mean, std and signal len calculated for each base in each k-mer after resquiggle was performed? I noticed that the TSV file output of the extract features module contains a list of comma separated values for the signal mean, std, signal len columns.

PengNi commented 5 years ago

Hi,

cent_signals are the central m (default 360) signals from the signals of each k-mer.

After re-squiggle, each base will get it's corresponding (usually 5-30) signals. Then we calculate the mean, std, length of the signals of each base.

You can check out our published manuscript (btz276) for more information.

Best, Peng