811dd66056e8ee6ceca4b67ea0551a0540ded944 hiram Thu Nov 10 11:15:09 2022 -0800 eliminate the bit about name searching no redmine diff --git src/hg/utils/automation/asmHubXenoRefGene.pl src/hg/utils/automation/asmHubXenoRefGene.pl index 8d8a6f3..90a17e7 100755 --- src/hg/utils/automation/asmHubXenoRefGene.pl +++ src/hg/utils/automation/asmHubXenoRefGene.pl @@ -59,36 +59,30 @@ <p> The RefSeq mRNAs gene track for the $assemblyDate $em${organism}$noEm/$asmId genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank"> GenBank</a>. </p> <h2>Track statistics summary</h2> <p> <b>Total genome size: </b>$totalBases<br> <b>Gene count: </b>$itemCount<br> <b>Bases in genes: </b>$basesCovered<br> <b>Percent genome coverage: </b>% $percentCoverage<br> </p> -<h2>Search tips</h2> -<p> -Please note, the name searching system is not completely case insensitive. -When in doubt, enter search names in all lower case to find gene names. -</p> - <h2>Methods</h2> <p> The mRNAs were aligned against the $em${organism}$noEm/$asmId genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept. </p> <p> Specifically, the translated blat command is: <pre> blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl