cfd30ac6ff3e9e9d11d2f53e9290c88c4fed1e94 lrnassar Mon Apr 13 14:42:30 2020 -0700 Cleaning up what looked to have been accidentally duplicated entries, no RM diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 3c5b6b0..16dbf89 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -290,88 +290,30 @@ sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> <p> Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an "<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" target="_blank">analysis set</a>" version of the hg19 genome fasta file to our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> directory, and indexes for BWA, Bowtie2, and Hisat2.</p> <p> We would like to thank the Genome Research Consortium for creating the patches to hg19. We would also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest patch to hg19.</a> <a name="022720"></a> <h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (hg19/hg38)</h2> <p> -mitochondrial sequence, <a href="../../cgi-bin/hgTracks?db=hg19&position=chrMT:4277-5648" -target="_blank">chrMT</a>, to the assembly. We used GenBank sequence NC_001807 for chrM in hg19 and -earlier, but the sequence preferred by the community is the revised Cambridge Reference Sequence -(rCRS), <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" target="_blank">NC_012920</a>. The -new chrMT is the rCRS, NC_012920. <a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/" -target="_blank">Patch sequences</a> from -<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.14" target="_blank">GRCh37.p13</a> have -also been added to hg19.</p> -<p> -More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. -The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/latest/" -target="_blank">/latest</a> download directory on the downloads server. With the addition of new -sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> -<p> -Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an -"<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" -target="_blank">analysis set</a>" version of the hg19 genome fasta file to our -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> -directory, and indexes for BWA, Bowtie2, and Hisat2.</p> -<p> -We would like to thank the Genome Research Consortium for creating the patches to hg19. We would -also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest -patch to hg19.</a> - -<a name="022720"></a> -<h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (hg19/hg38)</h2> -<p> -mitochondrial sequence, <a href="../../cgi-bin/hgTracks?db=hg19&position=chrMT:4277-5648" -target="_blank">chrMT</a>, to the assembly. We used GenBank sequence NC_001807 for chrM in hg19 and -earlier, but the sequence preferred by the community is the revised Cambridge Reference Sequence -(rCRS), <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" target="_blank">NC_012920</a>. The -new chrMT is the rCRS, NC_012920. <a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/" -target="_blank">Patch sequences</a> from -<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.14" target="_blank">GRCh37.p13</a> have -also been added to hg19.</p> -<p> -More information on how patch sequences are incorporated can be found on the -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. -The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/latest/" -target="_blank">/latest</a> download directory on the downloads server. With the addition of new -sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> -<p> -Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an -"<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" -target="_blank">analysis set</a>" version of the hg19 genome fasta file to our -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> -directory, and indexes for BWA, Bowtie2, and Hisat2.</p> -<p> -We would like to thank the Genome Research Consortium for creating the patches to hg19. We would -also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest -patch to hg19.</a> - -<a name="022720"></a> -<h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (hg19/hg38)</h2> -<p> We are pleased to announce a new track, RefSeq Select+MANE, for the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr1&g=refSeqComposite">GRCh37/hg19</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=refSeqComposite">GRCh38/hg38</a> human assemblies. This track is a combination of NCBI transcripts with the <em>RefSeq Select</em> tag, as well as transcripts with the <em>MANE Select</em> tag. The result is a track with a single representative transcript for every protein-coding gene. The track can be found as part of the NCBI RefSeq composite track.</p> <p> <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">RefSeq Select</a> transcripts are chosen by an NCBI pipeline to be representative of every protein-coding gene. As part of the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/MANE/">MANE project</a>, however, RefSeq Select transcripts that have a 100% identical match to a transcript in the Ensembl annotation are given the MANE Select designation. In this way, MANE Select is a subset of RefSeq Select. It should be noted, however, that there are