eee955f8ef61e34b14de10a4887e267228439180 lrnassar Fri Jul 26 14:28:51 2024 -0700 Feedback from CR, refs #34147 diff --git src/hg/htdocs/cite.html src/hg/htdocs/cite.html index 9f0359e..b6ee1f1 100755 --- src/hg/htdocs/cite.html +++ src/hg/htdocs/cite.html @@ -29,31 +29,31 @@ scientific manuscript and ensure readers in 10 years can still find the DNA sequence that you analyzed. This requires mention of the assembly, chromosome position, any transcripts, and ideally also a Genome Browser stable link:

  1. Assembly: Provide a clear mention of which genome assembly you are working with, e.g. "hg19" or "hg38". It is often helpful to place the assembly name directly on any supplemental file names if they contain annotations. E.g. "promoters.hg38.bed".
  2. Chromosome Position: References to nucleotides should have full chromosome positions in the publication text or a supplemental table, whenever possible. Including only the position on the transcript or coding sequence can be confusing later as transcript models change. E.g. mention "NC_000023.11:g.32389644G>A", in addition to the transcript-based description "NM_004006.2:c.4375C>T". Or, in the manuscript, you can add the chromosome location in brackets, such as "(hg38,chr11:32389644)", when nucleotide 4375 of NM_004006.2 is discussed.
    3. -
  3. Transcript: Transcripts change. Always mention the accession of a transcript, not only the gene name. E.g "NM_004006.2", not just +
  4. Transcript: Transcripts change. Always mention the accession of a transcript, not only the gene name. E.g. "NM_004006.2", not just "the longest transcript of the gene DMD". Gene symbols and transcripts change over time, so any sort of accession is helpful.
  5. Stable links: A UCSC Genome Browser link is a great way to share results or regions of interest in a way readers and reviewers can explore. It includes the assembly, position, all transcripts, any tracks visible, all filter settings that you made and any other settings in the browser. If you would like to include a link, do not copy the URL directly from the address bar, the one with "hgsid=xxx". These links are long and expire after a few days. Instead, use the menu option "My Data > My Sessions", to generate a short, stable link to your current genome browser view. For more information on how to add your own annotations to share this way see Custom Tracks and Track Hubs.