d2a02f56a0e84d51213d44955b694ce7daace230 jnavarr5 Fri May 31 11:41:50 2019 -0700 Updating redirected links for hg18, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/yaleBertoneTars.html src/hg/makeDb/trackDb/human/yaleBertoneTars.html index 368d833..088ffd4 100644 --- src/hg/makeDb/trackDb/human/yaleBertoneTars.html +++ src/hg/makeDb/trackDb/human/yaleBertoneTars.html @@ -47,31 +47,31 @@ <A HREF="https://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE1904" TARGET=_blank>GEO accession</A> for details of experimental protocols.</P> <P> The TARs identified for hg13 (NCBI Build 31) were mapped to this assembly using Blat. The program pslCDnaFilter was used to filter alignments using the parameters <TT>-minId=0.96</TT>,<TT> -minCover=0.25</TT>, <TT> -localNearBest=0.001</TT>,<TT>-minQSize=20</TT>, <TT> -minNonRepSize=16</TT>,<TT> -ignoreNs</TT>,<TT> -bestOverlap</TT>.</P> <H2>Display Conventions</H2> <P> TARs are represented by blocks in the graphical display. The numeric part of the ID displayed when the track has pack or full visibility is the ID used by the Yale Database for Active Regions with Tools -(<A HREF="http://dart.gersteinlab.org/" TARGET=_blank>DART</A>). A link to +(<A HREF="http://papers.gersteinlab.org/papers/dart/" TARGET=_blank>DART</A>). A link to this database is provided on the details page for each TAR.</P> <H2>Data Analysis</H2> <P> Two groups of TARs were identified: Normal and Poly(A)-associated.</P> <H3>Normal TARs:</H3> <P> Clusters of transcription units were identified that consisted of at least five consectutive probes with fluorescence intensities in the top 90th intensity percentile and with genomic coordinates within a 250-nt window. After collecting these regions genome-wide, their locations were compared to those of annotated components of genes. As a result, a total of 13,889 transcription units, ranging in size from 209 to 3,438 nucleotides, @@ -105,25 +105,25 @@ In 94% (90/96) of cases, the PCR products were found to be of the expected size in a single-pass assay.</P> <H2>Credits</H2> <P> These data were generated and analyzed by a collaboration between the labs of Michael Snyder, <A HREF="http://bioinfo.mbb.yale.edu/" TARGET=_blank>Mark Gerstein</A>, and Sherman Weissman at Yale University and with NASA Ames Research Center (Moffett Field, California) and Eloret Corporation (Sunnyvale, California).</P> <H2>References</H2> <P> Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S <em>et al</em>. -<A HREF="http://science.sciencemag.org/content/306/5705/2242" +<A HREF="https://science.sciencemag.org/content/306/5705/2242" TARGET=_blank>Global identification of human transcribed sequences with genome tiling arrays</A>. <em>Science</em>. 2004 Dec 24;306(5705):2242-6.</P> <P> Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE <em>et al</em>. -<A HREF="http://science.sciencemag.org/content/306/5696/655" +<A HREF="https://science.sciencemag.org/content/306/5696/655" TARGET=_blank>A gene expression map for the euchromatic genome of <em>Drosophilamelanogaster</em></A>. <em>Science</em>. 2004 Oct 22;306(5696):655-60.</P>