IGV not showing transcripts

Hi, I have recently started using IGV and I have loaded the human (hg38) genome from their server. I am trying to view a gene that has 9 transcripts according to Ensembl, but IGV is showing 1 only even when I click expanded it doesn't show the transcripts. Any suggestions?
Thanks!

transcripts igv

• 3,201 views • link

updated 5.2 years ago by ATpoint

• written 5.2 years ago by shaden •

1 answer

Probably RefSeq is shown, which is the default. You would need to download an Ensembl reference and load it. A GTF file unless something can be downloaded directly via File -> Load From Server.

• 0 views • link

written 5.2 years ago by ATpoint

More posts like this

What database to use for GATK baseRecalibration when using the ensembl hg19 genome
written 2.2 years ago by ramiro.barrantes •

I am running gatk base recalibrator as part of a pipeline (sarek), and it requires --dbsnp` or `--known_indels. I am using the regular ensembl hg38.fa.gz …
small RNA seq data from human cell line only give me 0 counts
written 6.3 years ago by leandroteixeira •

I recently started working with RNA seq analysis and despite having some expertise in R, I'm very new in the linux environment! I've been trying …
IGV Fasta Error: Uneven Line Lengths
written 6.7 years ago by eds35016 •

I'm trying to import my reference genome into IGV so that I can view an alignment but IGV doesn't seem to like my reference fasta. …
Ensembl: Genes versus Transcripts
written 8.1 years ago by nathaniel.schleif •

Going under the Ensembl one can look up particular genes as well as particular transcripts. In the process of doing so you can view the …
PacBio amplicon sequencing
written 8.3 years ago by williamsbrian5064

Hi, Someone in my lab recently got some PacBio sequencing done on a single amplicon. We're trying to figure out how to even look at …
how can I see the coverage of my own BED file on UCSC Genome Browser?
written 9.1 years ago by sustcyucw •

I have several BED file of transcripts, and I want to see the coverage of them like IGV shows. But the IGV always crashed because …
Gene specific region visualization in Alignment (.bam) or Variant calling file (.vcf) in IGV
written 11.0 years ago by ravi.uhdnis

Hi, I have multiple whole genome alignment files (.bam of a human sample) and also have one variant calling file (.vcf) generated using GATK HaploTypeCaller, …
Problem Viewing Alignments in IGV When Loading Custom FASTA file
written 11.2 years ago by moldach

<p>IGV provides a number of genomes that are hosted for example Human hg18. When you load this data the default is set to view the …
View annotations in igv of bam file with multiple chromosomes
written 11.6 years ago by yellowbike •

I use IGV to view BAM files. Most times I'm viewing single chromosome genomes. When view single chromosomes I'm able to view annotations by making …
Does RefSeq DB have a CDS file for its transcripts?
written 11.7 years ago by pwg46

Hello, I am looking for a file which contains all CDS for their NM (coding transcript) identifiers. Ensembl has one which maps each of its …