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BIMSBbioinfo / ciRcus

An R package for annotation of circular RNAs
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implement merge_bed.py features #18

Open retaj opened 7 years ago

retaj commented 7 years ago

Would be very helpful if someone (@mschilli87? @marvin-jens?) could let me know what merge_bed.py was actually doing :) Checklist of features/functions sorted by importance? :winkwink:

mschilli87 commented 7 years ago
marvin-jens commented 7 years ago

Thanks, Marcel!

On Wednesday, March 8, 2017 10:05:46 AM EST Marcel Schilling wrote:

  • [ ] integrate columns in a 'meaningful' (tm @marvin-jens) way :wink:
retaj commented 7 years ago

You will be assigned to three issues for each funny comment :maggy:

mschilli87 commented 7 years ago

@marvin-jens would you have time for a skype call on friday? @greeco also offered to help out with finishing off find_circ2 if needed as he's using it now, too.

marvin-jens commented 7 years ago

Hi petar,

It is aggregating the information on each circ from multiple runs of find circ. So, read counts would be added up and you'd get a comma separated list of them in an extra column, matched by a sorted list of run/sample identifiers in the adjacent column. This, to me, was the main feature. Others is quality metrics: best uniqueness, or whatever we wanna use, should be max of all runs, for example. Does this help?

marvin-jens commented 7 years ago

Sounds good. What time? 10:30 EST would be good for me. Best, -Marvin

On Wednesday, March 8, 2017 11:05:37 AM EST Marcel Schilling wrote:

@marvin-jens would you have time for a skype call on friday? @greeko also offered to help out with finishign off find_circ2 if needed as he's using it now, too.

mschilli87 commented 7 years ago

sounds good to me @retaj, @greeco: what about you guys?

retaj commented 7 years ago

Sure, I'm joining!

marvin-jens commented 7 years ago

Hey guys, skype deactivated my account and their server seems down. How about whatsapp? Or wire?

On Wednesday, March 8, 2017 11:05:37 AM EST Marcel Schilling wrote:

@marvin-jens would you have time for a skype call on friday? @greeko also offered to help out with finishign off find_circ2 if needed as he's using it now, too.

mschilli87 commented 7 years ago

I have neither

mschilli87 commented 6 years ago

@retaj: Is this still on? I could try to make some time for this. Really shoudn't be that hard. Most work would probably defining a good set of test cases.