SEQanswers

Go Back   SEQanswers > Introductions



Similar Threads
Thread Thread Starter Forum Replies Last Post
Job Opportunity - Partners HealthCare Boston, MA - Senior Bioinformatician, PCPGM KW869 Academic/Non-Profit Jobs 0 02-15-2012 09:30 AM
Hiring now: Senior Bioinformatics Scientists NGS Applications - Boston area GenomeQuest Industry Jobs! 0 03-17-2011 02:18 AM
DAM-SIG 2010 | July 9 | Boston nekrut Events / Conferences 0 05-24-2010 12:58 PM
FindPeaks 3.1.3 (alpha) - ChIP-Seq and UCSC-compatible short-read wig track creator apfejes Bioinformatics 4 05-27-2008 12:44 PM
Workshop: Next-Generation Sequencing Data Management (April 28, 2008) in Boston chrisdag Events / Conferences 0 01-23-2008 01:33 PM

Reply
 
Thread Tools
Old 01-09-2010, 07:09 PM   #1
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default Hello from Boston (IGV creator)

Hi, I'm the creator if IGV (Integrative Genomics Viewer) and am joining the forum to keep abreast of active issues, takes suggestions from this community, and hopefully get some of my questions answered.

IGV can be used to visualize short-read alignments, as a generic genome browser, and for microarray based experiments. I'm still learning my way around this website, and will try to subscribe to some of the forums, but fill free to send me a private message re IGV questions.

Jim Robinson
Broad Institute
Jim Robinson is offline   Reply With Quote
Old 01-14-2010, 11:48 AM   #2
sdarko
Member
 
Location: Bethesda, MD

Join Date: Apr 2009
Posts: 51
Default

Hi Jim,

I caught your presentation at NIH on IGV recently. Great tool and I've been using it ever since.

Sam
sdarko is offline   Reply With Quote
Old 01-14-2010, 12:10 PM   #3
polivares
Member
 
Location: Manchester, UK

Join Date: Jan 2009
Posts: 29
Default

I want to thank you for the great tool you have developed !

You make me save LOTS of time.

All the best

Pedro
polivares is offline   Reply With Quote
Old 09-20-2010, 08:29 PM   #4
Buzz0r
Sequenizer
 
Location: Singapore

Join Date: Sep 2010
Posts: 27
Default

hey there,
i am thinking about using the IGV for my research but i am also considering the new SAVANT. is there a video of the talk you gave earlier this year at NIH? or any other presentation of the IGV?

thanks, thomas
Buzz0r is offline   Reply With Quote
Old 09-21-2010, 07:47 PM   #5
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi Thomas,

Sorry but we don't have any videotapes of presentations. I suggest you try both tools, choice is good and you might find you like both for different things.

-- Jim
Jim Robinson is offline   Reply With Quote
Old 09-21-2010, 11:30 PM   #6
Buzz0r
Sequenizer
 
Location: Singapore

Join Date: Sep 2010
Posts: 27
Default

okay,

we already are looking at both and see nice visual possibilities in either one. We are only using the viewers for inspection due to our own analytic and statistic scripts so i cannot comment on the further possibilitier like the analytical plugins for example.

But for other readers: both are very easy to handle and very good on the memory usage. I will update you if i find any big runtime, memory aso differences if there are any readers who are actually interested in this IGV vs. SAVANT comparison. I might also look at another viewer called "SVA" if i ever get enough spare time soon...schedule is packed as usual ...

best, thomas
Buzz0r is offline   Reply With Quote
Old 09-22-2010, 05:59 AM   #7
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Very good. If you test any really large data files, such as "wig" files, you should use "igvtools" to convert the ascii file to a .tdf file. These are more or less equivalent in purpose to the ".savant" files, but it is optional to create these in IGV so many people don't know about them. You can run igvtools from the command line or launch a GUI to run them from the file menu. This format is used for all the large tracks in our "hg18" load from server, such as the Encode data.
Jim Robinson is offline   Reply With Quote
Old 01-21-2011, 02:05 AM   #8
boetsie
Senior Member
 
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
Default

<<<MOVED THIS QUESTION TO Bioinformatics >>>

Hi Jim,

I'm currently testing IGV for visualising SNPs on a bacterial genome. I've generated a SNP table with CLC which looks like this;

Reference Position Consensus Position Variation Type Length Reference Variants Allele Variations Frequencies Counts
122 122 SNP 1 G 1 A 100 133
1411 1411 SNP 1 T 1 C 100 135
1639 1639 SNP 1 G 1 A 100 127
1738 1738 SNP 1 A 1 G 100 118
....

I have converted this file to a simple .bed file;

GENOMENAME 121 122 A
GENOMENAME 1410 1411 C
GENOMENAME 1638 1639 A
GENOMENAME 1737 1738 G
......

This all works, as i can read in the file and visualize it along the genome. However, i want to add more information, like the 'Frequences' and 'Counts' column. These columns should be displayed if i scroll over a SNP.

How can i do this? How should the input look like?

Thanks for the help,

Boetsie

Last edited by boetsie; 01-21-2011 at 02:11 AM.
boetsie is offline   Reply With Quote
Old 01-21-2011, 08:53 AM   #9
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi,

Unfortunately the bed format is pretty rigid in column definitions. One alternative is to us GFF3 (http://gmod.org/wiki/GFF3#GFF3_Format) and use the last column (attributes). So

1411 1411 SNP 1 T 1 C 100 135

would become

chrName . SNP 1411 1411 . . . ID=SNP1411;Name=C;Reference=T; etc

GFF is very verbose, you will have to repeat the attribute names on every row. You could also use VCF format, which IGV supports and is defined for this. Finally, I could add the snp table format, email a reference to the spec to igv-help@broadinstitute.org and we can discuss it further.

Regards,

Jim
Jim Robinson is offline   Reply With Quote
Old 01-21-2011, 02:26 PM   #10
Jean
Member
 
Location: Canada

Join Date: Nov 2008
Posts: 37
Default

Hi Jim,
I have been using IVG to view bacterial RNA-seq data and I really like the viewer. However, I am having trouble getting the gene annotation information to display. I have tried loading the GFF file with the genome FASTA but the track is blank - am I possibly doing something wrong?

Jean
Jean is offline   Reply With Quote
Old 01-21-2011, 03:59 PM   #11
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi Jean,

The most common cause of this is a mismatch in sequence (chromosome/contig/whatever) names between the fasta and GFF file. If you want to email us a sample of your GFF and fasta file I'll look at it in more detail. Send it to igv-help@broadinstitute.org.

-- Jim
Jim Robinson is offline   Reply With Quote
Old 01-22-2011, 05:34 PM   #12
gaffa
Member
 
Location: Gothenburg/Uppsala, Sweden

Join Date: Oct 2010
Posts: 82
Default

Hi Jim, I really like the IGV browser but one thing that could use some improvement in my opinion is the display of insertions. I don't know if there are any plans to change this, but the current system with the "I"-symbol marking the location of an insertion doesn't really allow for detailed examination of sequence context in/around insertions. Instead I usually resort to samtools tview for such examination.
gaffa is offline   Reply With Quote
Old 01-22-2011, 05:39 PM   #13
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Yes, that's embarrassing really. It was copied from UCSC's method of displaying insertions in multiple alignments until something better could be coded. Its high on my list to improve.

So the plan is to "stretch" the reference where insertions occur so that the whole sequence of the insertion can be seen. The reference sequence will just show dots there. It really is high on my list but there's a flood of other things being implemented at the moment, I expect to get to this within the next 6-8 weeks however.

-- Jim
Jim Robinson is offline   Reply With Quote
Old 01-24-2011, 02:48 PM   #14
Jean
Member
 
Location: Canada

Join Date: Nov 2008
Posts: 37
Default

Hi Jim.
I just wanted to thank you for the update to IGV to display my custom GFF file. We now have some really great visualization of our transcriptome mappings that will be invaluable for analysis.

Attached is a screenshot for anyone who might be interested.

I've also noticed I can enter annotation information into the file which is displayed in IGV by mouse-over - very useful!

Jean
Attached Images
File Type: jpg IGV_view.jpg (83.0 KB, 77 views)

Last edited by Jean; 01-24-2011 at 03:03 PM.
Jean is offline   Reply With Quote
Old 02-23-2011, 04:51 AM   #15
doron
Junior Member
 
Location: Israel

Join Date: Feb 2011
Posts: 2
Default Gff3 problems

Hi Jim,

great work on the IGV, it is very helpful!
I have a small problem with viewing gff3 data.
I attached an example of a gene i'm trying to view. (gene.gff3)
The viewer only shows 2 of 3 UTRs, with no CDSes.

I found a way to improve the situation by inserting an exon record (gene_improved.gff3)
But, In this example, the viewer shows only 1 of the 2 5UTRs.

Is there a way to show all UTRs (in narrow blocks) and Cdses (in thick blocks)?

Thank you very much!
Doron Shem-Tov
doron is offline   Reply With Quote
Old 02-23-2011, 04:54 AM   #16
doron
Junior Member
 
Location: Israel

Join Date: Feb 2011
Posts: 2
Default Adding attachments to last post

I hope this time it will attach...
Attached Files
File Type: txt gene.txt (524 Bytes, 17 views)
File Type: txt gene_improved.txt (602 Bytes, 9 views)
doron is offline   Reply With Quote
Old 02-28-2011, 07:16 AM   #17
Joker!sAce
Member
 
Location: Denmark

Join Date: Feb 2011
Posts: 21
Default

Hey, I'm using IGV too. I'm just starting on it and I like it, It's a great tool.
Joker!sAce is offline   Reply With Quote
Old 07-03-2011, 02:53 PM   #18
crisant
Junior Member
 
Location: Rio de Janeiro

Join Date: Mar 2010
Posts: 7
Default

Hi Jim, I started to use IGV and seems to be fantastic. I have maize RNAseq and sorghum RNAseq. For the first I used the built-in genome and was nice, no porblem with that. I would like now to mapp the sorghum reads and was nice too, but I can't see the genes in the lower window (I see the reads in the upper window). Let me explain what I did: I imported the sorghum genome in fasta and in the "gene file" I choosed a GGF file (Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff), but nothing appeared in the lower window. What I am doing wrong? Thanks for any help.
crisant is offline   Reply With Quote
Old 07-03-2011, 03:01 PM   #19
Jim Robinson
Member
 
Location: Boston, MA

Join Date: May 2009
Posts: 75
Default

Hi,

This problem is usually caused by a mismatch in the sequence (chromosome) names between the gff and fasta files. The fix is to either rename the sequence names in one of the files (usually the GFF), or create an alias table as described below (look at the bottom of the page).

http://www.broadinstitute.org/software/igv/LoadData

-- Jim
Jim Robinson is offline   Reply With Quote
Old 07-03-2011, 03:31 PM   #20
crisant
Junior Member
 
Location: Rio de Janeiro

Join Date: Mar 2010
Posts: 7
Default

Thanks Jim, resolved.
Regards
crisant is offline   Reply With Quote
Reply

Tags
genomics viewer, igv, visualization

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO