Details
-
Type:
Support
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Labels:None
Description
From: Alex Tonks <TonksA@cardiff.ac.uk>
Date: Wednesday, 10/1/14, 4:45 PM
To: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Subject: IGB Affymetrix
> Hi Loraine, I think this might be a bit of novice question but I am
>having
> trouble loading Affymetrix annotations-probe set alignments in IGB. I
> don¹t see the option to load the data in the IGB quickload or in the UCSC
> DAS.
> Any help is much appreciated
>
>
> Best wishes
>
> Alex
>
>
> _____________________________________________________
> Dr Alex Tonks
> Senior Lecturer,
> Fellow of the Higher Education Academy
>
> Centre of Excellence for Leukaemia and Lymphoma Research,
> Dept Haematology, School of Medicine
> Cardiff University, Heath Park, Cardiff
> CF14 4XN
> Tel: 02920742235
> Fax: 02920744655
Attachments
Issue Links
- relates to
-
IGBF-212 Make Affymetrix probe set visualization available as a data set option
-
- Closed
-
Activity
From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Wednesday, October 29, 2014 3:55 PM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue
Excellent thanks
Best wishes
Alex
From: Mason Meyer <mason.meyer@my.lr.edu>
Sent: Mon 11/3/2014 7:17 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: RE: IGB Affymetrix Issue
Hey Alex,
Sorry again for the delay on resolving your issue. My boss has put together a file for you that is available here:
https://bitbucket.org/lorainelab/affyprobesetsforigb/downloads
Open the file “GPL570.HG-U133_Plus_2.link.psl” into IGB (you can drag and drop right into IGB after selecting Homo sapien as your genome). When doing this, make sure the file with the .tbi extension is in the same directory as the the link.psl file.
My boss told me to include a few tips for you as well. You may want to configure the annotation file to display the ID field as the label field. Also, remember that you can combine the plus and minus strands if desired.
We wanted to send you this file so that you could use it now for your purposes but my boss is currently working on adding it to the IGB Quickload site as well, so in the future look for similar data files under the Affymetrix folder under the Data Access panel in IGB. Please let us know if anything seems odd or if you need help in displaying this file in IGB properly. Let us know how it works for you!
Thanks again,
Mason Meyer
From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Tue 11/4/2014 4:09 PM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue
Hi Mason,
Many thanks to yourself, your lab colleagues and Loraine. Your instructions were great and easy to implement. However the handy tip about ID display was the best!.
Thanks again-it works great and I am very appreciative.
Best wishes
Alex
From: Mason Meyer <mason.meyer@my.lr.edu>
Sent: Wed 11/5/2014 5:50 PM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: RE: IGB Affymetrix Issue
Hey Alex,
I hope the files that the team made for you are still suiting your needs. Ann (my boss) wanted me to get back in touch with you to let you know that when opening the file into IGB, you should probably use the “GPL570.HG-U133_Plus_2.link.psl.gz” file, which conatins the .GZ extension, as this will load faster. We’re very glad we had the opportunity to help you out. Please let us know if there is anything else we can do for you or any recommendations you may have that may help IGB evolve in the future.
Thanks again,
Mason Meyer
From: Alex Tonks <TonksA@cardiff.ac.uk>
Sent: Thu 11/6/2014 2:35 AM
To: Mason Meyer <mason.meyer@my.lr.edu>
Subject: RE: IGB Affymetrix Issue
Hi Mason,
Thanks again and please pass on my thanks to Ann.
Best wishes
From: Dr. Ann Loraine <Ann.Loraine@uncc.edu>
Date: Thursday, 10/2/14, 12:17 AM
To: Alex Tonks <TonksA@cardiff.ac.uk>
Subject: IGB Affymetrix
> Hello Alex,
>
> It is nice to hear from you!
>
> I¹m forwarding your question to Mason Meyer and Nowlan Freese who lead
>our
> IGB support efforts.
>
> Question: Which species and genome version are you working with? Also,
> which array are you interested in?
>
> Bad news: Affymetrix is no longer supporting access to probe set
> information in IGB, but we should be able to help. Probably you remember
> IGB has a very nice visualization of probe set design sequences and
>probes
> aligned on the genomic sequence. If we can get the probe and design
> sequence information from Affymetrix, we should be able to make the probe
> set visualization available as a data set option in IGB.
>
> Mason and Nowlan - the protocol for creating the track information is not
> complex, but we ought to document how to do it in the Developer's guide
>as
> it involves multiple steps. So we should probably add this as a ³to-do²
> item (task) in IGB Jira.
>
> Alex, just to fill you in: We use a web site (nicknamed IGB Jira) to keep
> track of our ³to-do² list for IGB. If you have suggestions for new
> features to add or suggestions on how to make the user interface more
> accessible, we would love to hear them and add them to IGB Jira. The IGB
> Jira record would cite you as the source of the idea, which may be useful
> for tenure and promotion purposes. But if you prefer that we not cite
> you, that is fine, too.
>
> If you are curious, you can see what we are working on for the next
> release of IGB here: http://jira.transvar.org.
>
> I look forward to hearing from you about the array and genome you are
> working with.
>
> Thanks for reaching out,
>
> Ann