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Psy-Fer / SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data
MIT License
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SquiggleKit can be used for extract raw current signal in specific position of read? #36

Open weir12 opened 4 years ago

weir12 commented 4 years ago

Hi Thank you for you developing & maintaining this project :) I noticed that squigglekit can extract the current signal for a particular motif. So,I just wonder if it can extract raw current signal in specific position(base index) of read? like,extracting a sequential current signal which is attributable to [i, j] interval base of foo.fast5 Thanks

Psy-Fer commented 4 years ago

Hello, Yes, I've thought of the same functionality, and it wasn't quite in the scope of squigglekit at the time of building it.

However, I have since built a library that does this along with a colleague of mine.

We plan to release it once I get our RNA barcoding review sent back off, and then some coronavirus work. (to give an idea of timeline). Should be a matter of weeks if you are willing to wait?

Otherwise, maybe we can work something out if you you need it faster than that.

I hope you are keeping safe throughout those pandemic.

James

weir12 commented 4 years ago

Thank you for your support and look forward to the launch of the new version. Wish you safety and get through the hard time.

jnhutchinson commented 2 years ago

Hi, did anything ever come of this? We are hoping to do something similar (i.e. extract regions by position into new fast5 files) for use in a training model.