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Studying the isomiR accurcy with NGS technology #27

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lpantano opened this issue Jan 17, 2019 · 27 comments
Open

Studying the isomiR accurcy with NGS technology #27

lpantano opened this issue Jan 17, 2019 · 27 comments
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@lpantano
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@lpantano @gurgese @ThomasDesvignes @mhalushka @mlhack @keilbeck @BastianFromm @ivlachos @TJU-CMC @sbb25 @phillipeloher @carriewright11 @arunhpatil

Hi all,

I am opening a new thread to organize the discussion of the tewari reanalysis.

Since now is the re-analysis of a lot of data, I change the tentative title of the project.

These are the minutes for today: https://github.com/miRTop/incubator/blob/master/tewari/minutes.md#01-17-2019

Next meeting 01-31-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

Thanks!
@lpantano
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Hi all,

Today's meeting was canceled.

Next meeting 02-14-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

I started the draft of what it would be the paper:

https://docs.google.com/document/d/1VQN_7j0omnzKNc566jfe39stZVhXsfG2feNEkaJ4cFc/edit

And I created the 16 spikeins that are unique between them and not mapping to any reads detected in the tewari data:

https://github.com/miRTop/incubator/blob/master/unique_synthetic_sample/spikeins16.fa

Ioannis is working in the big set.

My collaborator will test the fragment analyzer, but it seems won't have enough resolution.

Thomas and I discussed and maybe northern blot would be better but somebody should try it first. Any volunteers?

I know Carrie is trying to validate some sequences are being detected everywhere by PCR.

Thanks!

@lpantano
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Hi all,

just to remind that the next meeting is this Thursday at 10am.

Next meeting 02-28-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

Thanks

CC new people in case they are interested: @FlorianThibord
Link: https://github.com/miRTop/incubator/tree/master/tewari

@FlorianThibord
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Hi,
Thank you, it looks very interesting, I'll be available thursday.

@lpantano
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Hi all,

I will have to cancel tomorrow's meeting since I was sick last week and I had to re-schedule my visit to sRNAlytic, hopefully, this will help us. I will send some notes when I am back.

Next meeting 03-28-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

I hope we have a bunch of important updates for that day!

Thanks! happy spring break for professors/students in this side of the ocean :)

@lpantano
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lpantano commented Apr 8, 2019

Hi all,

minutes for the last meeting are here:https://github.com/miRTop/incubator/blob/master/tewari/minutes.md#03-28-2019

I am going to cancel this week meeting since I will be away for one week. Feel free to chime in here with an urgent update:

  • Ioannis, did you find a company for the synthetic sequences?

Next meeting: Next meeting 04-25-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

cheers

@lpantano
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Hi all,

I have to cancel the meeting again. I started a new job and I am having unexpected meetings. I will send an email in a couple of hours to regroup and hopefully we can meet next week.

Sorry about this. I just got news about the other meeting that i really need to be.

Cheers

@lpantano
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Hi all,

sorry again to have to cancel the meeting.

Let's try to meet on May 9 as scheduled to avoid messing with people's calendar.

Next meeting: Next meeting 05-09-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

I added the two keypoints of our analysis to http://bit.ly/mirtop-isomirs-meta-analysis at the beginning of the documents. I added all the data I could found that tested different methods and synthetic and real samples.

This makes us have to discuss about the limitation of the data and discuss about the future of the project. Because of that, the agenda points will be:

  • Ioannis, update on the synthetic experiment
  • Discussion to see if we can find money to make the replicates experiment (targeting up to 10 reps)
  • Realistic future of this analysis

Thanks all, I promise I won't cancel again. It has been a hard month for me but I am coming back to normality.

Please, come to the meeting.

Thanks!

@lpantano
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Hi all,

if nobody has an update, I'll cancel tomorrow's meeting. @ivlachos , do you have any updates?

I will continue with the research note format, but I won't have anything until end of June.

Thanks!

@mhalushka
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I have nothing to add.

@ivlachos
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I was waiting for further information but didn't get any. So nothing to add.

@carriewright11
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carriewright11 commented May 23, 2019 via email

@lpantano
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lpantano commented Jun 5, 2019

No updates from my side yet. Congrats to Carrie to get her paper out! I will add her data to the meta-analysis.

If nobody has updates we skip to 20th June.

Next meeting: Next meeting 06-20-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

Cheers

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@lpantano
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lpantano commented Jun 5, 2019

No updates from my side yet. Congrats to Carrie to get her paper out! I will add her data to the meta-analysis.

If nobody has updates we skip to 20th June.

Next meeting: Next meeting 06-20-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

Cheers

@ivlachos
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ivlachos commented Jun 5, 2019

We're finalizing the synthetic sequence selection. We might have our first results tonight, so we could discuss a bit tomorrow. However, It's still work in progress, so I don't know if everything will be ready for tomorrow.

@lpantano
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lpantano commented Jun 5, 2019 via email

@lpantano
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Hi all,

we are meeting tomorrow to discuss some updates.

Talk to you tomorrow.

Next meeting: Next meeting 06-20-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@lpantano
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lpantano commented Jul 3, 2019

of course not meeting tomorrow :) happy 4th of july.

Next meeting: Next meeting 07-18-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@lpantano
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Hi,

I got very sick, so I will cancel the meeting. I have been busy with the mirtop paper, so not much update on my side. Ioannis, if you have something and want to share it, I can start the meeting and then leave.

If any other person has any update, please post here.

cheers

Next meeting: Next meeting 08-01-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@ivlachos
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ivlachos commented Jul 18, 2019 via email

@mhalushka
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Only new news is my collaborator, Matt McCall, is interested in isomiR analysis and I told him about this group. He might engage to do some analysis with some new ideas. I will be at a meeting 8/1 so will be missing the next meeting.

@lpantano
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lpantano commented Jul 19, 2019 via email

@lpantano
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I'll keep tomorrow's meeting.

Little updates with new members and some analyses going on right now.

See you!

Next meeting: Next meeting 08-01-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@lpantano
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lpantano commented Aug 1, 2019

Hi all,

We got updates on the synthetic oligos that would cover the same space than the real ones, but without mapping to any of the human,rat,mouse miRNAs.

Ioannis will ask for a quotation for oligos.

I finished the re-analysis of almost all the samples, here is the link with the new update and anybody can download the data to play around: https://github.com/miRTop/isomir_accuracy_meta_analysis.

Next meeting: Next meeting 08-15-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@lpantano
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A reminder of tomorrow's call. We'll keep this one to introduce new people and get updates of the ongoings analyses.

Cheers

@BastianFromm
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BastianFromm commented Aug 15, 2019 via email

@lpantano
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I forgot to mention that today there is a meeting, but since I didn't confirm maybe nobody shows up. I will connect just in case.

If nobody comes, then:

Next meeting: Next meeting 09-12-2019, 10am EST time, 4pm GMT+1 time. (https://zoom.us/j/553765969)

@lpantano
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We have the meeting tomorrow at 10am EST TIME.

https://zoom.us/j/553765969

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@FlorianThibord @lpantano @mhalushka @carriewright11 @ivlachos @BastianFromm