7072384d5e6f4228bec4186d3d677527be0c9bc5 mspeir Fri Jun 26 09:37:20 2026 -0700 Adding data access to hs1 pages on the RR, refs # diff --git src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html index 608b3875357..0bc7959a80c 100644 --- src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html +++ src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html @@ -1,106 +1,131 @@ <h2>Description</h2> <p> This track represents the gene models for the T2T CHM13 assembly generated using the CAT (Comparative Annotation Toolkit) software with genes that CAT could not be mapped as well as novel paralogs, filled in from the LiftOff mappings. The reference annotations are from GENCODE V35. </p> <h2>Display Conventions and Configuration</h2> <p> This track follows the display conventions for <a href="https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction tracks</a>. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Gene names are displayed in 'pack' or 'full' mode. More information about each gene can be found by clicking on the specific gene/transcript model. </p> <p> The following color key is used: </p> <ul> <li><span bgcolor="rgb(255,51,255)">Blue</span>: protein coding</li> <li><span bgcolor="rgb(85,212,76)">Green</span>: non-coding</li> <!-- <li><span>Purple</span>: novel predictions from PacBio Iso-Seq and LiftOff</li> --> <li><span bgcolor="rgb(76,85,212">Pink</span>: pseudogenes </ul> <h2>Methods</h2> <p> This tracks combines gene annotations generated by two methods. First the Comparative Annotation Toolkit (CAT) was used to Liftoff was then used as a second annotation method to map genes missed by CAT and additional gene paralogs. </p> <h4>Comparative Annotation Toolkit</h4> <p> Genome annotation for T2T CHM13 assembly was performed using Comparative Annotation Toolkit (CAT). CAT leverages whole-genome alignments generated by Cactus to transfer annotations from one source genome to one or more target genomes. For this annotation set, CAT lifted over the reference GENCODE v35 annotations onto the T2T genome. CAT also incorporated Iso-Seq data, first assembled into transcripts with StringTie2, to make the final consensus annotation set.</p> <h4>Liftoff</h4> <p> Liftoff uses Minimap2 to align reference gene DNA sequences to the target genome and selects the alignment(s) concordant with the intron/exon structure with the highest sequence identity. A minimum sequence identity of 95% was required to annotate gene paralogs. After running Liftoff, we identified genes that did not overlap any CAT annotations using bedtools intersect. These were combined with the CAT annotation to create the final annotation. </p> +<h2>Data Access</h2> +<p> +The raw data can be explored interactively with the +<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. The data can also be +accessed from scripts through our <a href="https://api.genome.ucsc.edu" target="_blank">REST +API</a>, where the track name is <tt>catLiftOffGenesV1</tt>.</p> +<p> +For automated analysis, the data may be downloaded from our +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/catLiftOffGenesV1/" target="_blank">download +server</a> as a bigGenePred file. The file for this track is called +<tt>catLiftOffGenesV1.bb</tt>. Individual regions or the whole genome annotation can be obtained +using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a +precompiled binary for your system. Instructions for downloading source code and binaries can be +found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" +target="_blank">here</a>. The tool can also be used to obtain only features within a given range, +for example:</p> +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/catLiftOffGenesV1/catLiftOffGenesV1.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt> +<p> +Please refer to our +<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing +list archives</a> for questions, or our +<a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more +information.</p> + <h2>Credits</h2> <p> This track was provide by Marina Haukness <a href="mailto:mhauknes@ucsc.edu"><mhauknes@ucsc.edu></a> of UC Santa Cruz and Alaina Shumate <a href="mailto:ashumat2@jhmi.edu"> <ashumat2@jhmi.edu></a> of Johns Hopkins University. </p> <h2>References</h2> <p> Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/29884752" target="_blank"> Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation</a>. <em>Genome Res</em>. 2018 Jul;28(7):1029-1038. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29884752" target="_blank">29884752</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028123/" target="_blank">PMC6028123</a> </p> <p> Stanke M, Diekhans M, Baertsch R, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank"> Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>. <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a> </p> <p> Stanke M, Steinkamp R, Waack S, Morgenstern B. <a href="https://www.ncbi.nlm.nih.gov/pubmed/15215400" target="_blank"> AUGUSTUS: a web server for gene finding in eukaryotes</a>. <em>Nucleic Acids Res</em>. 2004 Jul 1;32(Web Server issue):W309-12. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15215400" target="_blank">15215400</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC441517/" target="_blank">PMC441517</a> </p> <p> Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank"> Progressive Cactus is a multiple-genome aligner for the thousand-genome era</a>. <em>Nature</em>. 2020 Nov;587(7833):246-251. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank">33177663</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673649/" target="_blank">PMC7673649</a> </p> <p> Shumate A, Salzberg SL. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33320174" target="_blank"> Liftoff: accurate mapping of gene annotations</a>. <em>Bioinformatics</em>. 2020 Dec 15;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33320174" target="_blank">33320174</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289374/" target="_blank">PMC8289374</a> </p>