File Changes for cline

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• src/hg/makeDb/doc/hg19.txt
  • lines changed 15, context: html, text, full: html, text
    Updating the commands for setting up the Rfam data used by UCSC Genes. Now that we're getting Rfam coordinates from the Rfam team, this process is a whole lot simpler
  • lines changed 5, context: html, text, full: html, text
    Changed the Rfam parsing to generate BED 12 data rather than BED 6
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 10, context: html, text, full: html, text
    Fixing the bug described in Redmine # 411, Question #10, on size discrepancies between the sequence in knownGeneTxMrna and the alignment in kgTargetAli. Lo and behold, the executable txCdsToGene makes occasional changes to the gene structure and outputs a new bed file, but txGeneProtAndRna (which creates ucscGenesTx.fa) wasn't working with this new bed file but was working with the outdated file
  • lines changed 16, context: html, text, full: html, text
    Setting up UCSC Genes for Round 3. Two differences from last time: (1) we now getting Rfam coordinates from the Rfam group, so the Rfam processing is greatly simplified, and (2) the related genomes include now sacCer3 instead of sacCer2, and ce6 instead of ce9 (that last one had been an error)
  • lines changed 17, context: html, text, full: html, text
    Updated the Rfam repository. We are now getting hg19 genomic alignments from the Rfam group, so we no longer have to re-derive the Rfam regions. This not only simplifies our own processing (greatly), it puts the ball in the Rfam court if any user takes exception with any of the Rfam hits
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 5, context: html, text, full: html, text
    In response to Redmine # 5002, Question # 9: added a brief description of the knownToRefSeq table and how its content differs from the RefSeq portion of kgXref
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Added a search stanza for Old UCSC Genes, so that you can search for name for old UCSC Genes transcripts in the Position/Search box