Question: cannot see tracks in IGV
0
gravatar for jeffmann131
2.7 years ago by
jeffmann1310 wrote:

Am trying to come to terms with IGV - currently feeling like a Bio-Dwarf-Star - am following the manual at ebook page 1001-1002 loading the Ebola sequence and gene annotation file - am confident this is correct and the sequence is successfully loaded, i.e. the .fa file - the sequence track is all OK. Also the gene annotation appears to load (no errors stated) and the track is labelled. However, there are no glyphs showing, i.e. no blue bars showing the visual representation of the genes. Also I tried loading the .bam file - same result. Have been at this for hours and can't get it to work. Any suggestions welcome. Thanks!!!!!

tool software error • 2.0k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by jeffmann1310
1

did you try to zoom at the base level ?

ADD REPLYlink written 2.7 years ago by Pierre Lindenbaum130k

Hi Pierre - yes can see the sequence ACGT etc but tracks are still blank (white holes)

ADD REPLYlink written 2.7 years ago by jeffmann1310

Can you post a screenshot of what you see?

ADD REPLYlink written 2.7 years ago by dariober11k

thanks have to figure out how to do that - am attempting right now

ADD REPLYlink written 2.7 years ago by jeffmann1310

sorry cannot figure out how to add screenshot file - all I can say is that the tracks are blank regardless of sequence resolution - also the genes annotation file appears to be correct, i.e. the lines with genes were extracted as shown below which is a copy and past of the .gff file when I open with a text-editor

AF086833    EMBL    gene    56  3026    .   +   .   ID=AF086833.3;gene=NP
AF086833    EMBL    gene    3032    4407    .   +   .   ID=AF086833.9;gene=VP35
AF086833    EMBL    gene    4390    5894    .   +   .   ID=AF086833.13;gene=VP40
AF086833    EMBL    gene    5900    8305    .   +   .   ID=AF086833.20;gene=GP
AF086833    EMBL    gene    8288    9740    .   +   .   ID=AF086833.34;gene=VP30
AF086833    EMBL    gene    9885    11518   .   +   .   ID=AF086833.41;gene=VP24;note=putative
AF086833    EMBL    gene    11501   18282   .   +   .   ID=AF086833.47;gene=L
ADD REPLYlink modified 2.7 years ago by genomax89k • written 2.7 years ago by jeffmann1310

Hi Genomax - thank you very much for this - I will work through your solution and let you know how I go (it may take me some time) - cheers, Jeff

ADD REPLYlink written 2.7 years ago by jeffmann1310

For future ref. Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 2.7 years ago by genomax89k
0
gravatar for genomax
2.7 years ago by
genomax89k
United States
genomax89k wrote:

I recently helped someone fix this. See this thread: C: IGV custom genome/Biostarhandbook Chapter 16

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by genomax89k
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