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• Human reference genome - remapping coordinates
  We tried remapping the genomic coordinates of hg19 to hg38 using NCBI Remap. We got some of the l...
• What is the name of this build What is equivalent to build37.fa.bz2
  Hi everyone So sorry if it is a naiive thing, but I am still new: What is name of this build: ...
• Reasons why genome coordinates may not have a relative between reference genome assemblies
  I was wondering why might it be that a given coordinate in say, hg19, may not map to any coordina...
• Does any large resequencing project have a genuinely hg38 VCF?
  In one of our projects we are comparing hg19-related assemblies (such as b37 etc) to hg38, and ba...
• Missing SNP in gnomAD hg38 liftover vcfs
  Hi, On gnomAD website there are both hg19 and hg38 vcf. hg38 vcfs are liftover from hg19. https:...
• Mapping percent difference between hg38 and hg19
  Hey, Is it normal that I have a drop of ~10% mapping using hg38 compared to hg19? I mean I mapp...
• Human genome with masked endogenous viral sequences
  Do you know where is possible to find a version of hg19 or hg38 with masked endogenous viral sequ...
• Do I need to use hg19 or hg38 reference for performing variant calling analysis and RNAseq analysis?
  Dear All, I need some help on selecting the reference fasta for human genome. Do I need to use h...
• Visualizing hg19 and hg38 FPKMs in a single plot
  Hello everyone, I am trying to plot `NCAM1` gene expression from 5 disparate RNA sequencing data...
• Is GRCh37 and hg19 are the same?
  I would like to visualise some of my bam files on IGV, the reference genome used to analyse was G...
• Problems when exporting GRanges file as bigwig after hg38 to hg19 lift over using rtracklayer and annotation hub
  I'm trying to use `rtracklayer` and `AnnotationHub` in `R` to lift over a `.bw` file I have that ...
• What is the difference between GRCh37 and hs37? And hg19?
  Hi! I've been struggling with the naming conventions of human reference genomes... I know hg19 a...
• why do bed files not contain information about the reference?
  Let's say I have a transcript NM_12345 whose first exon starts at position 1000 on chromosome 15 ...