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  • New Genes on GRCh38

    Hi everyone, I was wondering if anyone has the list of ~100 genes that have been added to the GRCh38 reference model (and not present in GRCh37) or knows how I can obtain them. Examples of such genes have been mentioned here:

    In an earlier blog post, we discussed how sequence updates in GRCh38, the most recent version of the human reference genome, filled in a gap in human chromosome 17 near position 21,300K and expanded the region by 500K (500,000 base pairs). In this post, we will again consider this same region, but with an emphasis … Continue reading Sequence updates in human assembly GRCh38: improving gene annotation →


    Much appreciated,
    Fouad

  • #2
    You could "diff" the GTF files for the two builds to see if you can find the additional genes.

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    • #3
      #!/bin/bash
      wget ftp://hgdownload.soe.ucsc.edu/golden...refGene.txt.gz -O refGene.hg19.txt.gz
      wget ftp://hgdownload.soe.ucsc.edu/golden...refGene.txt.gz -O refGene.hg38.txt.gz
      diff <(zcat refGene.hg38.txt.gz | cut -f13 | sort | uniq) <(zcat refGene.hg19.txt.gz | cut -f13 | sort | uniq) | grep "<" | awk '{printf "%s ",$2}END{print(" ")}'


      results ...
      CCDC187 COPG2IT1 ERVW-1 LINC01348 LOC100131532 LOC100653233 LOC103021296 MIR1268B MIR1273D MIR1285-1 MIR1285-2 MIR151A MIR1587 MIR297 MIR3159 MIR4448 MIR548E MIR562 MIR576 MIR582 MIR584 NFE4 OR8U9 PCAT14 PRSS2 RAB7B RN7SK RN7SL1 RN7SL2 RNA18S5 RNA28S5 RNA5S1 RNA5S10 RNA5S11 RNA5S12 RNA5S13 RNA5S14 RNA5S15 RNA5S16 RNA5S17 RNA5S2 RNA5S3 RNA5S4 RNA5S5 RNA5S6 RNA5S7 RNA5S8 RNA5S9 RNU105B RNU105C RNU1-1 RNU1-2 RNU1-27P RNU1-28P RNU1-3 RNU1-4 RNU2-1 RNU2-2P RNU4-1 RNU4-2 RNU5A-1 RNU5B-1 RNU6-1 RNU6-10P RNU6-14P RNU6-15P RNU6-21P RNU6-23P RNU6-26P RNU6-30P RNU6-36P RNU6-39P RNU6-42P RNU6-45P RNU6-46P RNU6-55P RNU6-56P RNU6-58P RNU6-59P RNU6-63P RNU6-68P RNU6-7 RNU6-75P RNU6-8 RNU6-82P RNU6-9 RNU7-1 RNVU1-1 RNVU1-14 RNVU1-15 RNVU1-17 RNVU1-18 RNVU1-3 RNVU1-4 RNVU1-6 RNVU1-7 RNY1 RNY3 SNORA73A SNORD112 SNORD113-3 SNORD113-8 SNORD118 SNORD13 SNORD14A SNORD14B SNORD14C SNORD14D SNORD14E SNORD3A SNORD3B-1 SNORD3B-2 SNORD3C SNORD3D TAS2R45

      The link you provided has little relevance to this list.

      Genes like HYDIN were really two genes; they were so similar(?) that they couldn't resolve them to two genes.

      A more sophisticated analysis might involve , for instance, seeing what genes map to one location in hg19, but map to two locations in hg38.
      Last edited by Richard Finney; 10-22-2015, 06:07 PM.

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