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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How to export the list of soft-clipped regions from a region of interest in IGV
I want to export the list of soft-clipped regions into a csv file from a region of interest in IGV. Additional information regarding the soft-clipped sequence, coordinate and nucleotide length will be ...
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What does the IGV refseq genes with three different thicknesses of lines mean?
What does the IGV refseq genes with three different thicknesses of lines mean?
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Searching for HLA-B in DNA results
I'm trying to find the HLA-B*15:01 variant in my DNA results, prompted from this research paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142661/#:~:text=HLA%2DB*15%3A01%20is%20strongly%...
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How to analyze an IGV alignment
I'm working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that ...
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What does presence/absence of black lines mean in IGV?
IGV (Integrated Genome Viewer) is a popular open-source tool for viewing alignment files. In my BAM file in IGV, some deletions have black lines running through them, and others don't. What causes ...
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Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?
I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these ...
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How can I convert codon coordinates to genomic position?
I am looking for a given mutation in IGV, which accepts coordinates in the form of
chr<X>:<Y>
Where X is the chromosome number and Y is the base ...
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Accessing .bam/.cram files from AWS S3?
What's the best/easiest way for accessing .bam/.cram files from S3?
I have .bam/.bai .cram/.crai and .bed + .gff files that I want to make available easily to others so they can browse in IGV and ...
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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.
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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 ...
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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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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 ...
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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 ...
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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 ...
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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:
...
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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 ...
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How to create a .bed file from .fasta? [duplicate]
I have some problems in creating a .bed file for hg19, so I will be able to visualize the .bed file in IGV.
The .fasta file contains rows of this form:
...
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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.
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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 ...
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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 ...
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