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cnv_from_bam's Introduction

About me

Hi! I'm currently (10/11/2022) a post-graduate researcher at the University of Nottingham working on adaptive sampling with nanopore sequencing. I'm interested in all sorts of Bioinformatics, visualisations and fun side projects ( Some of which I even complete ).

Current mood

Current Projects

๐Ÿฑโ€๐Ÿ’ป I'm currently working on:

minoTour - real-time monitoring of nanopore sequencers

Swordfish - An inter-communicator for minoTour and readfish

Advent Of Code ๐ŸŽ…๐ŸŽ… - Just gotta love it

๐Ÿ”ญ How to reach me:

Follow me on twitter for utter silence @rorymatics โ—ฆ Follow me on mastadon [email protected] โ—ฆ Open issues! โ—ฆ ๐Ÿ“ง [email protected]

cnv_from_bam's People

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cnv_from_bam's Issues

Option to fix bin width

At present this tool calculates bin width by calculating read starts per bin and holding that as a constant. It would be very useful to have an option for fixing bin width (which could
be dynamically changed) and let the number of reads per bin vary.

Directory of BAM file iteration

  • Do it
  • Add check that we aren't adding a new reference into the BAM file? This way we don't have to iterate the ref seqs every single time

Get Variance out for each chromosome

SIngle value measure of CNV

Ideas

  • Provide example of calculating it with np.variance
  • Implement in rust and return as a value on the cnv_result struct

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