b88f5b43c268c4d47e083b461e2565060cd144a7 max Fri Jul 17 06:03:18 2020 -0700 tiny change to genes faq, no redmine. Also adding track docs pages for wuhCor1 contacts track, refs #25910 diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 5ea3d01..dea3073 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -311,37 +311,39 @@ <p> RefSeq gene transcripts, unlike GENCODE/Ensembl/UCSC Genes, are sequences that can differ from the genome. They need to be aligned to the genome to create transcript models. Traditionally, UCSC has aligned RefSeq with BLAT (UCSC RefSeq sub-track) and NCBI has aligned with splign. The advantages of the UCSC alignments are that they are updated more frequently and are available for older assemblies (like GRCh37/hg19), but they are not placed manually to a chromosome location and are not the official alignments. Therefore, we recommend working with the NCBI annotations. When an assembly has an "NCBI RefSeq" track, we show it by default and hide the "UCSC RefSeq" track. </p> <p> NCBI transcripts are manually tied to a chromosome band or location. The advantage is that when there are two almost-identical transcripts in RefSeq, each one will be -placed to the official reference location in the NCBI annotations. For example, +placed at the official reference location in the NCBI annotations. For example, the transcript NM_001012276 has three almost-identical possible placements to the genome in the UCSC RefSeq track (as it is entirely alignment-based), -but NM_001012276.3 is shown at a single location in the NCBI RefSeq track. It -may be good to know about the almost-identical alignments when doing genomics -analysis, but for clinical reporting purposes, it is preferable to use the NCBI -RefSeq track. +but NM_001012276.3 is shown at a single location in the NCBI RefSeq track, as the NCBI +software will only retain the splign alignment at the manually annotated location. It +may be good to know about almost-identical alignments when doing genomic +analysis or manual inspection of NGS read alignments, but for clinical +reporting purposes or other automated analyses, we strongly recommend to use +the NCBI RefSeq track. </p> <p> In some rare cases, the NCBI and UCSC exon boundaries differ. Activating both RefSeq and UCSC RefSeq tracks helps you investigate the differences. Activating the RefSeq Alignments track shows NCBI's splign alignments in more detail, including double lines where both transcript and genomic sequence are skipped in the alignment. When available, the RefSeq Diffs subtrack may be helpful too. The upcoming <a target=_blank href=https://ncbiinsights.ncbi.nlm.nih.gov/2018/10/11/matched-annotation-by-ncbi-and-embl-ebi-mane-a-new-joint-venture-to-define-a-set-of-representative-transcripts-for-human-protein-coding-genes/>MANE gene set</a> will contain a set of high-quality transcripts that are 100% alignable to the genome and are part of both RefSeq and Ensembl/GENCODE but at the time of writing this project is at an early stage. </p> <p>