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Bioinformatics

Questions tagged [igv]

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

26 questions
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1 vote
1 answer
218 views

I want to know where a certain sequence occurs in my genome in IGV. I searched by "Tools --> Find Motif". Two new tracks appeared ("<sequence>" and " Negative"), ...
antbirdINFINITY's user avatar
  • 63
2 votes
0 answers
25 views

I am simply trying to follow the documentation here: https://igv.org/doc/igvjs/#Reference-Genome/ and test UCSC GenArk assembly GCA_000002305.1 with the following code (tracks removed to avoid ...
Pasquale Sada's user avatar
  • 121
1 vote
0 answers
82 views

I have a question regarding visualising ATACseq peaks and transcription factor binding sites. I uploaded bigwig files to IGV and I am wondering if there is a way to label transcription factor binding ...
giegie's user avatar
  • 11
1 vote
0 answers
94 views

I am having an issue understanding some records for VCF file. We are analyzing human samples to detect somatic cancer mutations. We have a duplicate sample that was processed using Illumina Dragen ...
Skepto18's user avatar
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1 vote
1 answer
58 views

I have a web-based application that does variant calling and offers the option of opening a bam file using either IGV or JBrowse, both running as integrated webapps, not desktop applications. Some of ...
terdon's user avatar
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1 vote
1 answer
69 views

This is a BAM file from a 30x coverage Nebula Genomics test opened with IGV. I found an area (1:30169255-30169600) where the coverage is less than 15x. Can I interpret it as a part of one strand of ...
if0615's user avatar
  • 21
0 votes
0 answers
108 views

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 ...
vive's user avatar
  • 1
5 votes
1 answer
1k views

What does the IGV refseq genes with three different thicknesses of lines mean?
huangzj's user avatar
  • 63
3 votes
2 answers
456 views

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%...
stan's user avatar
  • 131
3 votes
0 answers
859 views

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 ...
pythonbeginner44's user avatar
  • 81
1 vote
1 answer
698 views

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 ...
TimD1's user avatar
  • 312
1 vote
0 answers
111 views

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 ...
Dan's user avatar
  • 136
3 votes
1 answer
467 views

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 ...
PedroD's user avatar
  • 143
2 votes
3 answers
706 views

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 ...
719016's user avatar
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1 vote
1 answer
2k views

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
MudithMMBc's user avatar
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