• Ensembl chromosome name?

    Hi 

    I am using Ensembl genome references.  Ensembl chromosome names don't have the 'chr' prefix ...

  • GRCh38 BAM with hg38 VCFs

    I have a BAM file containing an alignment to the GRCh38 "analysis pipeline" set with decoys (from...

  • Looking for neanderthal genomes to download

    EDIT:
    Since the data I'm looking for isn't available, my new question is if it's possible to conc...

  • Chromosome naming convention: Why are there chromosomes named "1" and "1A"?

    I've been stumbling on multiple genome of birds where there is a "1A" chromosome and a "1" chromo...

  • Getting list of chromosome names from indexed BAM file

    Given an indexed BAM file, is the following command guaranteed to give the full and correct listi...

  • Beagle 4 & Beagle 3.3.2 [Java Error]

    Hi,

    This is probably a fairly simple question... I recently downloaded Beagle 4 as it was fairly...

  • All chromosomes for mapping?

    Hi,

    I'm still getting to know STAR and wanted to ask you, if you just use Chromosomes 1 to 22 an...

  • Question: From A List Of Gene Symbols To A Bed File With name of the chromosome and Start/end position

    Hi,y'all,
    I have a list of Gene Symbols,How can i transform Gene Symbols to a .bed file with name...

  • What is this result from samtools idxstats?

    When running samtools idxstats on an indexed BAM file foo.bam in order to build a list of chromos...

  • SNPEff database building error

    java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
    There might be...

  • Find closest gene to chromosome location

    Hello!

    I started a gene enrichment analysis (I haven't done this before), and I have a dataset t...

  • Chromosome Names in genome are incompatible with annotations

    Dear community,

    while creating an index for the bovine genome with STAR, the process fails becau...



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