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Studying the isomiR accurcy with NGS technology #27

Open lpantano opened 5 years ago

lpantano commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

lpantano commented 5 years ago

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 commented 5 years ago

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:

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

cheers

lpantano commented 5 years ago

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 commented 5 years ago

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:

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 commented 5 years ago

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 commented 5 years ago

I have nothing to add.

ivlachos commented 5 years ago

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

carriewright11 commented 5 years ago

I also have nothing to add.

Get Outlook for iOShttps://aka.ms/o0ukef

On Wed, May 22, 2019 at 9:04 PM -0400, "ivlachos" notifications@github.com<mailto:notifications@github.com> wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/miRTop/incubator/issues/27?email_source=notifications&email_token=AFPS2Y6SQFVJD6GZHY7YFRDPWXUS7A5CNFSM4GQ2KQ42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWAYUMY#issuecomment-495028787, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFPS2Y73PD6URKVCTIMRH33PWXUS7ANCNFSM4GQ2KQ4Q.

lpantano commented 5 years ago

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

lpantano commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

Thanks! Let’s meet in two weeks so you have more time. :)

On June 5, 2019 at 12:55:05 PM, ivlachos (notifications@github.com) wrote:

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.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/miRTop/incubator/issues/27?email_source=notifications&email_token=AAML6HHPQHYRSWBXQTLIJITPY7VWRA5CNFSM4GQ2KQ42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXALATY#issuecomment-499167311, or mute the thread https://github.com/notifications/unsubscribe-auth/AAML6HEGDMOYUBAPVW3TJRLPY7VWRANCNFSM4GQ2KQ4Q .

lpantano commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

Hi Lorena,

No problem.

No big news from our side. We’re waiting for various replies.

I’ll touch base probably within next week with an update.

Best,

Ioannis

From: Lorena Pantano notifications@github.com Reply-To: miRTop/incubator reply@reply.github.com Date: Thursday, July 18, 2019 at 9:28 AM To: miRTop/incubator incubator@noreply.github.com Cc: Ioannis Vlachos ivlachos@lessr.eu, Mention mention@noreply.github.com Subject: Re: [miRTop/incubator] Studying the isomiR accurcy with NGS technology (#27)

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)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

mhalushka commented 5 years ago

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 commented 4 years ago

Thanks Marc. Thanks for bring Matt to the group. Looking forward to new ideas.

See you in two meetings, then.

lpantano commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

Cheers

BastianFromm commented 4 years ago

Thanks for a nice meeting! Please let me know if I could be of help.

On a another (but not unrelated!) note I'd like to share with you our latest preprint on the second version of mirgenedb.org

https://www.biorxiv.org/content/10.1101/258749v2

I would be happy about any comments and thoughts on how to incorporate this for our mirna format project.

Bastian

Lorena Pantano notifications@github.com schrieb am Mi., 14. Aug. 2019, 23:09:

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

Cheers

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/miRTop/incubator/issues/27?email_source=notifications&email_token=AGQCFX764SBY7UFU42RLWYLQERYBRA5CNFSM4GQ2KQ42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4KDYCQ#issuecomment-521419786, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQCFX63M4XMO2CJHNSTYF3QERYBRANCNFSM4GQ2KQ4Q .

lpantano commented 4 years ago

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 commented 4 years ago

We have the meeting tomorrow at 10am EST TIME.

https://zoom.us/j/553765969