d5932e4051a4885f0036831cdfc5fbf1eb08a499 lrnassar Tue Oct 10 17:16:27 2023 -0700 Fixing broken blog links, refs #32439 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 08a4673..f86a9a9 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -423,54 +423,54 @@ <h6>What is chr_alt?</h6> <p> The chr_alt chromosomes, such as <em>chr5_KI270794v1_alt</em>, are alternative sequences that differ from the reference genome currently available for a few assemblies including danRer11, mm10, hg19, and hg38. These are regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. UCSC labels these haplotype sequences by appending "_alt" to their names. These alternative loci scaffolds (such as KI270794.1 in the hg38 assembly, referenced as chr5_KI270794v1_alt in the browser), are mapped to the genome and provide supplemental genomic information on these variable locations. To find the regions these alternate sequences correspond to in the genome you may use the <a href="../cgi-bin/hgTrackUi?db=hg38&g=altSeqLiftOverPsl" target="_blank">Alt Haplotypes track</a> if one is available. </p> <p> Additional information on alternative loci can be found on our <a -href="http://genome.ucsc.edu/blog/patches/" target="_blank">hg38 patches blog post</a> +href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">hg38 patches blog post</a> as well as the <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml#ALTERNATE" target="_blank">Genome Reference Consortium (GRC) website</a>. </p> <a name="downloadFix"></a> <h2>chr_fix chromosomes</h2> <h6>What is chr_fix?</h6> <p> The chr_fix chromosomes, such as <em>chr1_KN538361v1_fix</em>, are fix patches currently available for the mm10, hg19, and hg38 assemblies that represent changes to the existing sequence. These are generally error corrections (such as base changes, component replacements/updates, switch point updates or tiling path changes) or assembly improvements (such as extension of sequence into gaps). These fix patch scaffold sequences are given chromosome context through alignments to the corresponding chromosome regions. A list of all chromosomes including chr_fix sequences can be found in the <a href="../cgi-bin/hgTracks?db=mm10&chromInfoPage=" target="_blank">mm10</a>, <a href="../cgi-bin/hgTracks?db=hg19&chromInfoPage=" target="_blank">hg19</a>, or <a href="../cgi-bin/hgTracks?db=hg38&chromInfoPage=" target="_blank">hg38</a> assembly sequences pages. </p> <p> More information on these patch sequences can be found on our -<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">hg38 patches blog post</a> as well +<a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">hg38 patches blog post</a> as well as on the the <a href="https://www.ncbi.nlm.nih.gov/grc/help/faq/#fix-patches" target="_blank">Genome Reference Consortium (GRC) website</a>. </p> <a name="download10"></a> <h2>chrN_random tables</h2> <h6>What are the chr<em>N</em>_random_[table] files in the human assembly? Why are they called random? Is there something biologically random about the sequence in these tables or are they just not placed within their given chromosomes?</h6> <p> In the past, these tables contained data related to sequence that is known to be in a particular chromosome, but could not be reliably ordered within the current sequence.</p> <p> Starting with the Apr. 2003 human assembly, these tables also include data for sequence that is not in a finished state, but whose location in the chromosome is known, in addition to the unordered @@ -904,32 +904,32 @@ for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range using one of the hgdownload servers, example:</p> <ul> <li> North American server: <pre><code>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> </li> <li> European server: <pre><code>bigBedToBed http://hgdownload-euro.soe.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> </li> </ul> <p> -Read more in <a href="http://genome.ucsc.edu/blog/"> our blog</a> about -<a href="http://genome.ucsc.edu/blog/?s=programmatic">Accessing the Genome Browser Programmatically</a> +Read more in <a href="https://genome-blog.gi.ucsc.edu/blog/"> our blog</a> about +<a href="https://genome-blog.gi.ucsc.edu/blog/?s=programmatic">Accessing the Genome Browser Programmatically</a> to acquire data. </p> <p> <a name="snp"></a> <h2>How do I download dbSNP data?</h2> <p> For versions dbSNP153 and above, the data is formatted in bigBed files. Previous versions are MySQL tables. For help with versions before dbSNP153, see <a href="#download29">accessing MySQL data</a>. This FAQ entry pertains to versions dbSNP153 and above.</p> <p> Since dbSNP has grown to include over 700 million variants, the size of the All dbSNP (153+) subtrack can cause the <a href="/cgi-bin/hgTables" target=_blank>Table Browser</a> and <a href="/cgi-bin/hgIntegrator" target=_blank>Data Integrator</a> to time out, leading to a blank page or truncated output, @@ -1035,32 +1035,32 @@ target=_blank>dbSnpDetails.as</a> respectively. </p><p> UCSC has an <a href="/goldenPath/help/api.html" target=_blank>API</a> that can be used to retrieve values from a particular chromosome range. A list of rs# IDs can also be pasted/uploaded in the <a href="/cgi-bin/hgVai" target=_blank>Variant Annotation Integrator</a> tool in order to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc. </p><p> See our searchable <A HREF="https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/download+snps" target=_blank>mailing list archives</a> for more information and example queries. We also have information on -<a href="http://genome.ucsc.edu/blog/">our blog</a> about -<a href="http://genome.ucsc.edu/blog/?s=programmatic"> Accessing the Genome Browser Programmatically</a> +<a href="https://genome-blog.gi.ucsc.edu/blog/">our blog</a> about +<a href="https://genome-blog.gi.ucsc.edu/blog/?s=programmatic"> Accessing the Genome Browser Programmatically</a> to acquire data. </p> <a name="snpAlleles"></a> <h2>Why doesn't this SNP have two alleles?</h2> <p> When using the SNP tracks, some records may contain information about one or more alleles instead of the usual two alleles for the SNP. The following information should explain how this is possible.</p> <dl> <dt>One allele (i.e. reference only):</dt> <dd> The human genome reference has gone through many different assembly versions. The reference genome has always been a mosaic of sequences from multiple individuals, so it contains some rare or singleton mutations and is not entirely free of errors. Some SNPs were discovered on