Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Significance of Pindel's "AD" and finding SVs in IGV opulcy97 Bioinformatics 8 07-26-2013 10:12 AM
DEXSeq error in estimateDispersions: match.arg(start.method, c("log(y)", "mean")) fpadilla Bioinformatics 14 07-03-2013 02:11 PM
"Systems biology and administration" & "Genome generation: no engineering allowed" seb567 Bioinformatics 0 05-25-2010 12:19 PM
Startup "Knome" offers complete genome sequence for $350k! ECO Personalized Genomics 4 03-22-2010 07:12 PM
Discussion : "The diploid genome sequence of an Asian individual" edge Literature Watch 8 09-09-2009 06:31 PM

Thread Tools
Old 12-25-2013, 01:56 PM   #1
Senior Member
Location: Stanford

Join Date: Jun 2009
Posts: 181
Default IGV displays ">chr1 " as part of genome sequence

I was trying to figure out why all my chr1 alignments looked like they were full of mismatches in IGV, and then I noticed they were all off by 6 bp. I zoomed in to the beginning of chr1 to compare it with a FASTA file, and I saw this:

It looks like IGV somehow parsed the ">chr1 " header in the FASTA file as part of the sequence! Only chr1 is affected:

To verify that this wasn't something wrong with my downloaded genome, I removed it and re-downloaded it, but the problem persists. Then I tried downloading some other genomes.

mm10 is affected:

and hg19:

but not hg18, which was preinstalled:

I've reproduced this problem on two different computers using IGV versions 2.3.20 and 2.3.25. Is anyone else seeing this? Is it a bug? It doesn't seem like the kind of thing that would escape everyone's notice; all the coordinates are off by 6.
jwfoley is offline   Reply With Quote
Old 12-31-2013, 07:06 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

I do not see the same problem. hg18 was the same as yours (no problem) and just now loading in hg19 and mm10 shows just the 'N's at the start of chr1. Perhaps there was a problem on the 25th? I suggest reloading in the references.
westerman is offline   Reply With Quote


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 03:44 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO