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• Difference in BAM coverage between bedtools output and IGV coverage track
  Hi, I’m using bedtools to find regions of<20x coverage of target areas for a .BAM generated by...
• Whats the Difference between variants and SNPs in IGV?(or in general)
  I have a VCF file and a Bam file in IGV and am trying to find out what variants are have the loud...
• Export Coverage on IGV
  I have five different tracks on IGV from five sample alignment .bam files. I want to do more anal...
• how to visualize rna-seq coverage track in igv?
  Hello biostars community, how does one visualize an rna-seq coverage track alongside chip-seq bi...
• Visualize B-allele frequency on IGV for 2 samples
  Dear All, I have a non-standard task - visualize B-allele frequency tracks for 2 samples in 1 tr...
• IGV empty tracks render in blue
  I'm using IGV to display CNV data, and for some tracks there are no CNVs.. but for some reason IG...
• Colors in IGV
  I'm using IGV to visualize read coverage for a de novo trancriptome. Some of my mapped reads show...
• UCSC Viewer : Change color of the reads for stranded RNASEQ as IGV "first-of-pair-strand
  By default, UCSC show reads colored by read strand as show [here][1]. In IGV you can do the sam...
• Customize IGV coverage track in R
  Hi Biostars,   I want to recreate the IGV coverage track in R. I want to be able to customize an...
• IGV: Load custom data (chr, start, end, strand, sample)
  Hi, I've some data that I want to load into IGV. It represents some viral integration sites for ...
• Single-cell RNA-seq coverage track not corresponding to gene structure
  Hi, may be comeone can clarify the following things: I have a 10x data, which I processed through...
• how can I see the coverage of my own BED file on UCSC Genome Browser?
  I have several BED file of transcripts, and I want to see the coverage of them like IGV shows. Bu...
• Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS data
  OK. I realize this is not exactly a bioinformatics question but I know that a lot of people in th...
• Why IVG coverage track from bam and bigwig files looks different?
  Hi I am studying polyadenylation of ribosomal RNA in different yeast mutants. I am interested in ...
• visualizing RNAseq read coverage in Ensembl genome browser
  Apologies if this is somewhat basic - I usually work with smaller genomes and use local custom ge...
• IGV not highlighting possible variants
  Surely this is trivial, but I have looked everywhere and I cannot find the answer... IGV sometim...
• Stringtie2: how to interpret conflicts between results
  Hi, I am using Stringtie2 in order to obtain a better annotation of chicken genome (galGal6) us...
• Defining Region Of Interest Inside A Track In Igv
  Hi, I need to create a custom IGV track and force the software to visualize directly my region of...
• IGV tracks gene annotation
  Hi there, I'm trying to visualize a reference genome in IGV and annotate the genes using a custom...
• UCSC custom track - can different peaks have different color+height?
  Hi,  I want to build a custom UCSC track where different peaks have different color+height. I r...
• Export coverage Track from IGV
  Hi all, I would like to know if there is any way to get the total count of reads for each positi...
• IGV: highlight both primary and supplementary alignments of a read
  I'm using IGV and I grouped the alignments by supplementary tags Colored reads on the top panel a...