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  • Jan 31 2019 22:37

    bebatut on gh-pages

    Update on: Thu Jan 31 22:36:58 … (compare)

  • Jan 31 2019 22:00

    erasche on master

    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

  • Jan 31 2019 22:00
    erasche closed #1237
  • Jan 31 2019 22:00
    erasche commented #1237
  • Jan 31 2019 21:33
    jmchilton synchronize #1237
  • Jan 31 2019 21:01
    erasche labeled #1239
  • Jan 31 2019 21:01
    erasche opened #1239
  • Jan 31 2019 21:00
    natefoo opened #1238
  • Jan 31 2019 20:56
    jmchilton opened #1237
  • Jan 31 2019 20:17

    bebatut on gh-pages

    Update on: Thu Jan 31 20:17:17 … (compare)

  • Jan 31 2019 19:44

    erasche on master

    fix typos Merge pull request #1236 from g… (compare)

  • Jan 31 2019 19:44
    erasche closed #1236
  • Jan 31 2019 19:44
    martenson opened #1236
  • Jan 31 2019 19:44

    martenson on martenson-patch-2

    fix typos (compare)

  • Jan 31 2019 19:23

    bebatut on gh-pages

    Update on: Thu Jan 31 19:23:39 … (compare)

  • Jan 31 2019 19:06

    Slugger70 on master

    import some notes fix username and 1 more (compare)

  • Jan 31 2019 19:06
    Slugger70 closed #1234
  • Jan 31 2019 19:04
    erasche review_requested #1234
  • Jan 31 2019 19:03
    erasche synchronize #1234
  • Jan 31 2019 19:03
    erasche unlabeled #1234
pvanheus
@pvanheus
in the tutorial I'm writing at the moment I have an "Advanced" section on using the Rule Base Uploader instead of setting up collections manually. Is there a way to collapse this and only have it show if the reader clicks on something?
Saskia Hiltemann
@shiltemann:matrix.org
[m]
Make it a tip type box ?
pvanheus
@pvanheus
ok I'll have a look at how that renders...
Ana Sosa
@AnaSF_gitlab
Hello, can I ask if someone has gone through the Reference-based RNA-Seq data analysis training?
Saskia Hiltemann
@shiltemann
@AnaSF_gitlab go for it!
Ana Sosa
@AnaSF_gitlab
@shiltemann heh thanks, I'm on it :) I got an error and not sure how to proceed. so I'm wondering if someone is familiar with this training
Saskia Hiltemann
@shiltemann
A lot of people here are familiar with the training (and lots even helped write the tutorial), so if you describe your error I'm sure somebody can help you figure it out :) you've come to the right place for questions!
Ana Sosa
@AnaSF_gitlab
Oh ok! So I'm at the mapping point using the RNA STAR tool. The output gives an error that goes: Fatal INPUT FILE error, no valid exon lines in the GTF file: /srv/galaxy/shared/database/files/000/133/dataset_133966.dat
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.
So I understand that the .gtf file used for gene annotation does not contain the gene names in the same format, therefore not being able to compare
How can I change the name of one of the docs?
Lucille Delisle
@lldelisle
Indeed, probably you used a gtf from ensembl. Can you copy paste here the first lines of your GTF file?
Ana Sosa
@AnaSF_gitlab
The format gets all weird but here it goes
chr3R FlyBase gene 722370 722621 . - . gene_id "FBgn0085804"; gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene";
Lucille Delisle
@lldelisle
This is compatible with your genome. Do you have lines where the third field is "exon"?
Ana Sosa
@AnaSF_gitlab
Yes, there are gene, transcript, exon, CDS, start_codon...
I used the link listed in the training to download it
Lucille Delisle
@lldelisle
Did you choose the right genome then?
Ana Sosa
@AnaSF_gitlab
The training says to choose Fly (Drosophila Melanogaster): dm6 Full, which is no longer listed
there are 2 other options but none of them avoids this error from appearing
Lucille Delisle
@lldelisle
Which galaxy are you using?
Ana Sosa
@AnaSF_gitlab
.be (is this the question?)
Lucille Delisle
@lldelisle
Yes exactly.
Ana Sosa
@AnaSF_gitlab
I didn't know the reference genomes depended on the location of the server
Lucille Delisle
@lldelisle
Unfortunately for the moment, they do.
Ana Sosa
@AnaSF_gitlab
Okey, so I'll always get an error on this point as long as I'm in galaxy.be
Lucille Delisle
@lldelisle
For the moment yes.
Except if usegalaxy.be decide to install the new genome to support this training...
Helena Rasche
@hexylena:matrix.org
[m]
that should be in CVMFS, are they not using that?
Ana Sosa
@AnaSF_gitlab
@lldelisle thanks a lot for helping me understand the origin of the problem <3
@hexylena:matrix.org I'm not sure what that is, sorry
Lucille Delisle
@lldelisle
You are welcome.
@hexylena:matrix.org I don't know... Or they did not linked it to STAR...
image.png
There are only 4 choices in the last verison of STAR...
@AnaSF_gitlab , if you can, I would suggest to switch to usegalaxy.eu to do your training.
Meanwhile I will report that this genome is needed to make it work.
Ana Sosa
@AnaSF_gitlab
I filled the bugfix report but didn't pinpoint the exact origin of the problem
dannahjavens
@dannahjavens
For the Circos Tutorial, what is the link that we can use to create a Circos Plot through Galaxy?
2 replies
Ana Sosa
@AnaSF_gitlab
Hey @lldelisle , I got the answer from the admin team and they have just added the UCSC version of the D. melanogaster genome, which is called "Drosophila melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)" :)
Lucille Delisle
@lldelisle
:thumbsup:
vajiha12
@vajiha12
Hey I'm new here...Can anyone help me with namd please?
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Hi @vajiha12, what's your problem?
vajiha12
@vajiha12
Hi @gallardoalba:matrix.org i am trying to run md run using Google collab but i got an error
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG3RC1 CG2R51 NG3C51 (ATOMS 4692 4694 4698)
Can you help me with this?
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
Perhaps @chrisbarnettster or Simon Bray can help you.
vajiha12
@vajiha12
Ok thanks
Dave Clements
@tnabtaf
Hi All, just a reminder that all registration for GCC2021 closes in 2 hours. https://www.vibconferences.be/events/gcc2021-virtual-edition And Training Week starts Monday.
Rachel Rios
@rachelrios
Hey, how would I flag a spelling mistake? I don't think that calls for a whole bug fix in github.

"Sigmoid activation function can be used both at the output layer and hidden layers of a multilayer network. They allow the network to model non-linear realtionships between input and output."

realtionships -> relationships

Helena Rasche
@hexylena:matrix.org
[m]
Hey @rachelrios ! If it's such a small fix, you can always just correct it yourself, it's really easy, every page in the GTN has an "Edit this page on GitHub" button under the Extras menu?