2e3c89f43f3bb9d386178270200d0acce9fc8050 lrnassar Fri Nov 22 17:47:13 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/mouse/cloneEndSuper.html src/hg/makeDb/trackDb/mouse/cloneEndSuper.html index 19e72bc..87f9191 100644 --- src/hg/makeDb/trackDb/mouse/cloneEndSuper.html +++ src/hg/makeDb/trackDb/mouse/cloneEndSuper.html @@ -1,87 +1,87 @@ <h2>Description</h2> <p> This track shows the NCBI clone end predictions from the retired <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" target="_blank">NCBI Clone DB</a> database. Libraries with more than 20,000 clones are included in this track display. </p> <p> Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence.</p> <p> These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments.</p> <p> The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments).</p> <h2>Display Conventions and Configuration</h2> <p> Items in this track are colored according to their strand orientation. Blue indicates alignment to the forward strand, and green indicates alignment to the negative strand. </p> <h2>Methods</h2> <p> The mappings of these BAC end sequences are taken directly from the NCBI Clone DB FTP site <a href="ftp://ftp.ncbi.nih.gov/repository/clone/reports/Mus_musculus/" target=_blank>ftp.ncbi.nih.gov/repository/clone/reports/Mus_musculus/</A> *.GCF_000001635.22.103.*.gff files.</p> <p> UCSC filtered the NCBI Clone DB mapped ends to drop ends that mapped to a region that was three times longer than the median size of the clones in the library. Only libraries with more than 20,000 clones are included in this track display.</p> <table BORDER=1> <tr><th>library<br>name</th> <th>total<br>clones</th> <th>total end<br>sequences</th> <th>NCBI mapped<br>ends</th> <th>UCSC filtered<br>ends</th> <th>UCSC<br>dropped</th> <th>percent<br>dropped</th> </tr> <tr><th align=left><a href="https://dna.brc.riken.jp/en/cloneseten/b6n_bac_en" target="_blank">B6Ng01</A></th><td align=right>128,007</td><td align=right>253,638</td><td align=right>98,478</td><td align=right>95,837</td><td align=right>2,641</td><td align=right>2.68</td></tr> <tr><th align=left><a>bMQ</th><td align=right>129,826</td><td align=right>244,222</td><td align=right>75,671</td><td align=right>72,540</td><td align=right>3,131</td><td align=right>4.14</td></tr> <tr><th align=left><a >C3H</a></th><td align=right>86,696</td><td align=right>169,665</td><td align=right>43,690</td><td align=right>42,378</td><td align=right>1,312</td><td align=right>3.00</td></tr> <tr><th align=left><a href="https://bacpacresources.org/library.php?id=207" target="_blank">CH29</a></th><td align=right>93,023</td><td align=right>340,272</td><td align=right>52,320</td><td align=right>50,621</td><td align=right>1,699</td><td align=right>3.25</td></tr> <tr><th align=left><a >DN</a></th><td align=right>180,218</td><td align=right>665,070</td><td align=right>106,463</td><td align=right>100,472</td><td align=right>5,991</td><td align=right>5.63</td></tr> <tr><th align=left><a >MHPN</a></th><td align=right>118,658</td><td align=right>208,707</td><td align=right>61,942</td><td align=right>58,582</td><td align=right>3,360</td><td align=right>5.42</td></tr> <tr><th align=left><a >MHPP</a></th><td align=right>67,769</td><td align=right>112,081</td><td align=right>30,594</td><td align=right>28,550</td><td align=right>2,044</td><td align=right>6.68</td></tr> <tr><th align=left><a href="https://dna.brc.riken.jp/en/cloneseten/msm_bac_en" target="_blank">MSMg01</a></th><td align=right>175,178</td><td align=right>337,471</td><td align=right>83,677</td><td align=right>78,772</td><td align=right>4,905</td><td align=right>5.86</td></tr> <tr><th align=left><a href="https://bacpacresources.org/femmouse23.htm" target="_blank">RP23</a></th><td align=right>175,999</td><td align=right>553,274</td><td align=right>85,082</td><td align=right>83,062</td><td align=right>2,020</td><td align=right>2.37</td></tr> <tr><th align=left><a href="https://bacpacresources.org/mmouse24.htm" target="_blank">RP24</a></th><td align=right>163,859</td><td align=right>294,217</td><td align=right>52,470</td><td align=right>50,849</td><td align=right>1,621</td><td align=right>3.09</td></tr> <tr><th align=left><a >WI1</a></th><td align=right>907,213</td><td align=right>1,822,723</td><td align=right>337,591</td><td align=right>324,259</td><td align=right>13,332</td><td align=right>3.95</td></tr> </table> <h2>Credits</h2> <p> Additional information about the clone, including how it can be obtained, was available at the retired <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" target=_blank>NCBI Clone Registry</A>. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI's <a href="https://www.ncbi.nlm.nih.gov/genome/gdv/" target="_blank">Genome Data Viewer (GDV)</a> using the sequence data currently in Clone DB. Clone -DB users should refer to <a href="http://www.informatics.jax.org/" target="_blank">MGI</a> for their +DB users should refer to <a href="https://www.informatics.jax.org//" target="_blank">MGI</a> for their continuing research needs.</p> <p> Please <a href="mailto:info@ncbi. nlm. nih. gov">contact NCBI</a> with any comments, concerns, or if you need help with the use of Clone DB data.</p>