bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/FAQ/FAQreleases.html src/hg/htdocs/FAQ/FAQreleases.html index 7ebf837ec31..51f1f9223ec 100755 --- src/hg/htdocs/FAQ/FAQreleases.html +++ src/hg/htdocs/FAQ/FAQreleases.html @@ -376,31 +376,31 @@ The annotations accompanying an assembly are obtained from a variety of sources. The UCSC Genome Bioinformatics Group generates several of the tracks; the remainder are contributed by collaborators at other sites. Each track has an associated description page that credits the authors of the annotation.</p> <p> For detailed information about the individuals and organizations who contributed to a specific assembly, see the <a href="../goldenPath/credits.html">Credits</a> page.</p> <a name="asmEquivalent"></a> <h6>Which UCSC assemblies are equivalent to Ensembl or NCBI assemblies?</h6> <p> The asmEquivalent table on the hgFixed database is available on the public MySQL server to show which assemblies versions are identical (or almost identical) to each other between UCSC, Ensembl, Genbank, and RefSeq assemblies.</p> <pre> -mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -e 'desc asmEquivalent;' hgFixed +mysql --user=genome --host=genome-mysql.gi.ucsc.edu -A -e 'desc asmEquivalent;' hgFixed +----------------------+-------------------------------------------+ | Field | Type | +----------------------+-------------------------------------------+ | source | varchar(255) | | destination | varchar(255) | | sourceAuthority | enum('ensembl','ucsc','genbank','refseq') | | destinationAuthority | enum('ensembl','ucsc','genbank','refseq') | | matchCount | bigint(20) | | sourceCount | bigint(20) | | destinationCount | bigint(20) | +----------------------+-------------------------------------------+</pre> <p> The "Count" indications are the count of individual sequences in the assembly. When all three counts are identical, <code>matchCount == sourceCount == destinationCount</code>, then the match between genome assemblies is perfectly identical.</p> @@ -461,31 +461,31 @@ <h2>Differences between UCSC and NCBI mouse assemblies</h2> <h6>Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?</h6> <p> The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.</p> <a name="release5"></a> <h2>Accessing older assembly versions</h2> <h6>I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?</h6> <p> In addition to the assembly versions currently available in the Genome Browser, you can access the data for older assemblies of the browser through our -<a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</p> +<a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> page.</p> <a name="release6"></a> <h2>Frequency of GenBank data updates</h2> <h6>How frequently does UCSC update its databases with new data from GenBank?</h6> <p> GenBank updates for mRNA, RefSeq, and EST data occur on a semi-quarterly basis, following major NCBI releases. These updates are in place for most Genome Browser assemblies. Assemblies that are not on an incremental update schedule are updated whenever we load a new assembly or make a major revision to a table.</p> <p> <a name="release7"></a> <h2>Coordinate changes between assemblies </h2> <h6>I noticed that the chromosomal coordinates for a particular gene that I'm looking at have changed since the last time I used your browser. What happened?</h6> @@ -575,49 +575,49 @@ being stored as a MariaDb table. For very large queries, this may cause the Table Browser to timeout before the query finishes as dbSNP has grown to include over 700 million variants. If you find that your Table Browser query timesout for your list of rsIDs, you can use the <code>bigBedNamedItems</code> command-line tool to extract the rsID coordinates directly from the bigBed file instead of using the Table Browser.</p> <p>More information and examples using the <code>bigBedNamedItems</code> utility can be found on the following <a href="FAQdownloads.html#snp">FAQ entry</a>. As a reminder, you can run any Kent command-line tool without arguments to get the usage statement. </p> <a name="snpExtract"></a> <h6>How can I extract a list of rsIDs using chrom:start-end or vice versa?</h6> <p> Several utilities for working with bigBed-formatted binary files can be downloaded -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. Run a utility with no arguments to see a brief description of the utility and its options. </p> <ul> <li><b>bigBedInfo</b> provides summary statistics about a bigBed file including the number of items in the file. With the <b>-as</b> option, the output includes an autoSql definition of data columns, useful for interpreting the column values.</li> <li><b>bigBedToBed</b> converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. </li> <li><b>bigBedNamedItems</b> extracts rows for one or more rs# IDs.</li> </ul> <a name="snpExamples"></a> <h6>Examples:</h6> <ol> <li>Retrieve all variants in the region chr1:200001-200400 - <pre><tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> + <pre><tt>bigBedToBed http://hgdownload.gi.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout</tt></pre> </li> <li>Retrieve variant rs6657048 <pre><tt>bigBedNamedItems dbSnp155.bb rs6657048 stdout</tt></pre> </li> <li>Retrieve all variants with rs# IDs in a file (myIds.txt) and output to another file (dbSnp155.myIds.bed) <pre><tt>bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed</tt></pre> </li> </ol> <a name="release9"></a> <h2>Missing annotation tracks</h2> <h6>Why is my favorite annotation track missing from your latest release?</h6> <p> The initial release of a new genome assembly typically contains a small subset of core annotation