Questions tagged [igv]

Integrated Genome Viewer. GUI intended for the visualisation of genomic and transcriptomic data, along with annotations and other things.

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1answer
33 views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
2
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1answer
33 views

How can I not show insertions in the Integrative Genome Viewer (IGV)?

I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click ...
3
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1answer
59 views

How can I export a full alignment from IGV as an image?

The IGV browser lets you export an alignment as an image (File => Save Image). However, this image only contains those reads that fit in the viewing window: As you can see in the image above by ...
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0answers
19 views

How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV

We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we ...
2
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3answers
204 views

Hosting IGV web on a server

I have my analysis on a cloud server. The data is quite large, so copying it locally is not really an option. I want to be able to host IGV as a server on that server, so that it can access those ...
3
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1answer
234 views

What do the read colors in IGV mean?

I was looking at a bam file in the IGV viewer and saw: What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another ...
2
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1answer
77 views

Why does IGV turn a VCF QUAL of “.” into -10?

IGV is turning QUAL "." into -10 from this VCF of structural variations. I'm wondering if this means anything or if I should report a bug to the IGV devs. Here's a row from a VCF: ...
2
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2answers
160 views

Loading local FASTA file in igv.js

I'm trying to use igv.js for a very simple visualization of some genomic alignments, but I can't get past the first step. I have a FASTA file that I want to use as the reference, but igv.js ...
2
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5answers
1k views

How to create a .bed file from .fasta? [duplicate]

I have some problems with creating a .bed file for hg19 which I will be able to load on IGV. The fasta file contains rows of this form: ...
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0answers
111 views

igv_plotter error: Xvfb did not start

I am trying to get screenshots from alignments of reads to a genome in IGV (Integrated Genome Viewer) using igv_plotter. ...
3
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1answer
175 views

How to show only my read on IGV?

I have a large BAM file on my IGV. I'd like to visualize a read alignment. I have the read name, and I don't care anything else in the file. IGV has an option "Select by name" (see screenshot). The ...
3
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3answers
184 views

IGV jump to rsID location

Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box? For human and ...