Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

De novo transcriptome assembly, annotation, and differential expression analysis #1351

Merged
merged 22 commits into from Feb 13, 2020
Merged

De novo transcriptome assembly, annotation, and differential expression analysis #1351

merged 22 commits into from Feb 13, 2020

Conversation

@abretaud
Copy link
Collaborator

@abretaud abretaud commented Apr 26, 2019

Finally a tutorial for de novo transcriptome assembly, annotation, and differential expression analysis as promised in #59 .

It's different than the existing de novo transcriptomics as here we don't use a reference genome, we just assemble the transcriptome using Trinity

We (with @r1corre) have a first draft of workflow, but a few things are missing:

  • blast & co process before trinotate
  • trinotate visualization
  • better handling of data collections probably
  • find a good dataset
  • ...

Fixes #59
@hexylena
Copy link
Member

@hexylena hexylena commented Sep 12, 2019

@abretaud is this still in WIP?

Loading

@abretaud abretaud requested a review from as a code owner Nov 14, 2019
@lecorguille
Copy link
Member

@lecorguille lecorguille commented Nov 14, 2019

It's still in progress.

TODO :

  • Finish DE part
  • Annotation part
  • Text, Text, Question ...
  • Main questions
  • Main objectives
  • Main key_points
  • Satellite
    • data-library.yaml
    • tutorial.bib
  • ...
  • Full reading

Loading

@abretaud abretaud mentioned this pull request Nov 21, 2019
Closed
@lecorguille lecorguille mentioned this pull request Nov 25, 2019
Open
@lecorguille lecorguille changed the title [WIP] De novo transcriptome assembly, annotation, and differential expression analysis De novo transcriptome assembly, annotation, and differential expression analysis Feb 13, 2020
@lecorguille
Copy link
Member

@lecorguille lecorguille commented Feb 13, 2020

Can we consider to merge this PR?
I disabled the tutorial to get a nice URL we will be able to share tomorrow.

I promise to daily beat @r1corre to make him finish this tutorial 👿

Loading

bgruening
bgruening reviewed Feb 13, 2020
View changes
CONTRIBUTORS.yaml
@@ -540,6 +546,10 @@ workflow4metabolomics:
wm75:
name: Wolfgang Maier

xiliu:
name: Xi Liu
github: false
Copy link
Member

@bgruening bgruening Feb 13, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can you remove this @lecorguille

Loading

Copy link
Member

@lecorguille lecorguille Feb 13, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

AH ... how can I add Xi as author?

Loading

@shiltemann shiltemann merged commit cf64349 into galaxyproject:master Feb 13, 2020
1 of 2 checks passed
Loading
@shiltemann
Copy link
Member

@shiltemann shiltemann commented Feb 13, 2020

thanks @abretaud and @lecorguille! and good luck tomorrow!

Loading

@lecorguille
Copy link
Member

@lecorguille lecorguille commented Feb 13, 2020

Thanks!

Loading

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@lecorguille lecorguille

@shiltemann shiltemann

@bgruening bgruening

@galaxyproject/training-transcriptomics training-transcriptomics

Assignees
No one assigned
Labels
new contributor(s) new tutorial topic:transcriptomics work-in-progress
Projects
None yet
Milestone
No milestone
Linked issues

Successfully merging this pull request may close these issues.

RNASeq: de novo transcriptome assembly with Trinity
6 participants
@abretaud @hexylena @lecorguille @shiltemann @bgruening @bebatut