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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...
• 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 ...
• 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...
• 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...
• 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 ...
• IGV not highlighting possible variants
  Surely this is trivial, but I have looked everywhere and I cannot find the answer... IGV sometim...
• 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...
• 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...
• 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...
• 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 color interpretation by insert size
  Hi everyone, I am looking at RNAseq data in IGV. I have colored the reads by insert size: https:...
• Single-cell RNA-seq coverage track not corresponding to htseq-count output or IGV gene annotations?
  I have some single-cell RNA-seq data that I've processed via a `tophat2` --> `htseq-count` pip...
• Color / mark specific sequence bases differently in IGV
  Sometimes I've interested in highlighting specific positions within the sequence fields of a BAM ...
• Igv Coverage Track Display
  Hi, does anyone here know how to reverse the coverage track in IGV? I have separate the reads m...
• How can I use Samtools to map coverage distribution?
  I want to use Samtools to map copverage distribution and retrieve the regions with the highest co...