198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/sessions.html src/hg/htdocs/goldenPath/help/sessions.html index 59b50dbeefd..0e4ae60659b 100755 --- src/hg/htdocs/goldenPath/help/sessions.html +++ src/hg/htdocs/goldenPath/help/sessions.html @@ -102,31 +102,31 @@ target="_blank"><center><img width="70%" height="70%" src="../../images/session.hg19.split2.png"></center></a> <p> Using the multi-region exon-only feature available under the top blue menu bar and View selecting "Multi-Region" you can remove introns adjusting padding down to just one base (or none) to more clearly see the split codon above.</p> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html --> <h3>Examples of Different Codon Numbering in the hg19 Assembly</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.codonNums" target="_blank"><center><img width="70%" height="70%" src="../../images/session.hg19.codonNums.png"></center></a> <p> -The above session helps illustrate the how same region in an exon can have different codon +The above session helps illustrate how the same region in an exon can have different codon numbering reflecting different isoforms and that it is important to use caution when reading codon numbers in the literature. Here is an additional view of the region zoomed out 300x to display <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.codonNums2" target="_blank">the alternate splicing</a>.</p> <!-- Topic Division --> <a name="evolution"></a> <h2>Evolution</h2> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html --> <h3>Examples of Codon Wobble in the hg19 Assembly</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.wobble" target="_blank"><center><img width="70%" height="70%" @@ -228,31 +228,31 @@ within the golden path and shows X-linked colorblindness as a recombination hotspot in the opsin region where genes encode for light absorbing visual pigments.</p> <p> Another example featuring the Segmental Dups track is the <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.segDup2" target="_blank">15q11 Prader-Willi region</a> in which same-chromosome duplications lead to gain and loss of copies and a rare genetic disorder when some genes are deleted or unexpressed.</p> <!-- Topic Division --> <a name="tfbs"></a> <h2>Expression/regulation: TFBS/RNA-seq/ChIP-seq</h2> <!-- Session INFO: This comes from https://users.soe.ucsc.edu/~kuhn/workshops/jamesMadison2015/education.html --> -<h3>Microarray Probset data in the hg19 Assembly</strong></h3> +<h3>Microarray Probeset data in the hg19 Assembly</strong></h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.microArray" target="_blank"><center><img width="70%" height="70%" src="../../images/session.hg19.microArray.png"></center></a> <p> The above session uses the <a href="../../cgi-bin/hgTrackUi?db=hg19&g=genotypeArrays" target="_blank">Microarray Probesets</a> track to display Affymetrix, Agilent, and Illumina probe information.</p> <!-- Session INFO: This comes from the ENCODE index.html --> <h3>View ENCODE data (2003 - 2012) in the UCSC Genome Browser</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/encodeDemonstration" target="_blank"><center><img width="70%" height="70%" src="../../images/encode/browser.png"></center></a> <p> The above session highlights some key integrated track data from the ENCODE project including @@ -280,31 +280,31 @@ src="../../images/session.hg19.Dnase.png"></center></a> <p> This session comes from a question about how the DNaseI Hypersensitivity Clusters track is generated. <a href="https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/mwPp41nqVWw/c7QdhdLCwvgJ" target="_blank">The response</a> explains that the clusters track represents the combining and filtering of multiple DNaseI Hypersensitivity Uniform Peaks tracks in an attempt to summarize multiple individual experiments, which also can be viewed individually in the browser.</p> <h3>Example of how the Transcription Factor ChIP Track is generated from multiple experiments</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.TFBScluster" target="_blank"><center><img width="70%" height="70%" src="../../images/session.hg19.TFBScluster.png"></center></a> <p> This session helps illustrate the process behind creating the TFBS Clusters track. Uniform -processing resulted in a comparable signal scores viewable in the wgEncodeAwgTfbsUniform track, +processing resulted in comparable signal scores viewable in the wgEncodeAwgTfbsUniform track, that was then used to generate the clustered score in the wgEncodeRegTfbsClusteredV3 track, where a normalization factor was used to attempt to better distribute scores evenly. The session originated from a question regarding whether it was correct to interpret the darker score as increased biological evidence of binding for a transcription factor at a particular spot. <a href="https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/FPZuwGAuWoI/Hn00L0SPRUAJ" target="_blank">The response</a> shared how by filtering to display only the JUN, JUNB, JUND, and MYC factors you can see several individual "Uniform ...c-Myc" tracks displayed below the clusters track. Those are the separate wgEncodeAwgTfbsUniform tracks used to generate the processed clustered summary wgEncodeRegTfbsClusteredV3 track for this MYC cluster. Those individual uniform processed scores were used to create the cluster score given to the MYC cluster. Like the MYC factor, you can also click the JUN factors and you will see there is only one observed cell type where this data indicates this factor binds at this location. And similarly below, you will see the "Uniform... Jun" tracks that contributed to the clusters track.</p> <!-- Topic Division --> @@ -319,31 +319,31 @@ <p> A user was interested in an intron of the gene PHKB where a repeat element for AluY was given. The user could not find the Alu repeat, and <a href="https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/_X1bURBW8ho/TRs18-kez2AJ" target="_blank">the response</a> was to aid the user in turning on the RepeatMasker track where information on repeats, such as the AluY element desired, is contained.</p> <h3>Example of refGene exonFrames coming from mRNA</h3> <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg38.refGeneFrame" target="_blank"><center><img width="70%" height="70%" src="../../images/session.hg38.refGeneFrame.png"></center></a> <p> A user had written some code to generate exon frame data from the refGene table, based on the belief that the exonFrames should be possible to derive entirely from the cds{Start,End} and exon{Starts,Ends} by taking differences and dividing by three for the size of codons. However, the -user noticed an inconsistency with the their generated exonFrames output compared to the information +user noticed an inconsistency with their generated exonFrames output compared to the information in the refGene table. In <a href="https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/XRdN33qDvug/iTAZPUYksUsJ" target="_blank">the response</a> the explanation was that the exon frames come from the mRNA, not the genome, and the example provided (NM_001282171/KIR3DS1) represented a transcript where there were deletions in respect to the reference at chr19_KI270922v1_alt:123,732-123,733.</p> <pre>aacaga..agtgaacagc 000870 |||||| |||||||||| >>>>>> aacagaacagtgaacagc 123743 </pre> <p> By clicking into the details of the RefSeq gene NM_001282171 transcript and clicking the first link in the section titled "mRNA/Genome Alignments" one can see the alignments of the mRNA to the genome and find the dots <code>aga..agt</code> indicating a deletion.</p> <a name="more"</a> <h2>More information about sessions</h2>