[Loris-dev] LORIS first steps

[Xavier Lecours Boucher, Mr]

Hi,


Thank you for your interest in using LORIS. First of all, our genomic-browser module is in a beta version and still have room for improvements. I will try to answer you questions assuming you downloaded and install version 19.0 or 19.1


"Is there a specific team that I can contact for support?"

That would be me.


"I wan't to know what kind of file format are used to upload in LORIS?"

Under the file tab in the genomic browser you can upload a specific format for Methylation beta-values, or any Other. Selecting the first one will trigger the importation of the file content after some validation. For the Other category it will simply store the file on the file system. Both will move the file under /data/loris/data/genomics/ (this path can be changed in the configuraion module).


"Is there a readme ..."

Yes: https://github.com/aces/Loris/tree/v19.0.1/modules/genomic_browser


"which help to understand the Demo?"

Not yet. There is an help section in the top right corner of the screen but it is really limited. Here a brief overview


The genomic browser is divided into 6 tabs:

  *   Profile: This tab show a list of PSCID (subject ID) and the available omic data for each of them under the Files,SNPs, CNVs and CPGs columns.
  *   GWAS: This tab is intended to present GWAS results (a list of snps + annotations and the associated p-value) (this is empty on the demo site)
  *   SNP: A table where each row is the genotype of a PSCID at a given snp + that snp's annotations.
  *   CNV: A table where each row is a PSCID's observed variation, its location and additional information about that variation.
  *   Methylation:  A table where each row is the beta value of a PSCID at a given cpg + annotations of that cpg
  *   Files: A list of files uploaded with that module


For most of theses tabs, it is possible to display more columns in the table by selecting "All fields" in the Display drop down.


"I tried to upload a csv file but the system gives an file format error"

I will need a more specific error message to help. There might be limitations in the file size and/or type due to apache configurations. (see the README for a list of susceptible options)


I hope this shed some light

Please contact me for any questions, comments and/or request.


- Xavier Lecours

LORIS Developer


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Ousmane Diallo <ousmane.diallo3 at mcgill.ca>
Sent: April 25, 2018 8:43 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] LORIS first steps

Hi,
I have installed LORIS and want to see how it can help in manasing our
samples. My aim is to analyse SNP, CNV from GWAS data.
First, to understand the LORIS web interface I tried to use the Demo,
but I don't understand much about it. I don't know which files are used
and which data are compareted to what? I tried to upload a csv file but
the system gives an file format error.
I wan't to know what kind of file format are used to upload in LORIS? Is
there a readme which help to understand the Demo. Is there a specific
team that I can contact for support?


--
Ousmane Diallo
Bioinformatics specialist
Guy Rouleau laboratory
MNI - McGill University
514-398-6761
ousmane.diallo3 at mcgill.ca


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