7bcdb99907195a9c5eb9e4909d9d66d067addb0c
jnavarr5
  Mon Mar 31 15:00:37 2025 -0700
Fixing a spacing issue on the FAQgenes.html page, no Redmine.

diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html
index f646cf0d008..04bb7f4bdc9 100755
--- src/hg/htdocs/FAQ/FAQgenes.html
+++ src/hg/htdocs/FAQ/FAQgenes.html
@@ -412,31 +412,33 @@
 for either NCBI or BLAT to get the correct alignment and gene model because the genome sequence is
 missing for part of the gene.  NCBI and BLAT find slightly different exon
 boundaries at the edge of the problematic region. NCBI's aligner tries very hard
 to find exons that align to any transcript sequence,
 so it calls a few small dubious "exons" in the affected genomic region.
 GENCODE V19 also used an aligner that tried very hard to find exons, but it
 found small dubious "exons" in different places than NCBI.
 The <a target=_blank href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">RefSeq Alignments</a> 
 subtrack makes the problematic region very clear with double lines
 indicating unalignable transcript sequence.
 </p>
 <b>Data format:</b> <p>A small difference is the data format, which matters if you integrate our files into pipelines:
 The refGene table qName field stores the RefSeq accession but without the version number. The
 ncbiRefSeq tables show the full accession, with the version number. To add the version number 
 to the refGene table, use a MySQL command like this: <pre>
-SELECT matches,misMatches,repMatches,nCount,qNumInsert,qBaseInsert,tNumInsert,tBaseInsert,strand,concat(qName, '.', gbSeq.version),qSize,qStart,qEnd,tName,tSize,tStart,tEnd,blockCount,blockSizes,qStarts,tStarts from refSeqAli, hgFixed.gbSeq WHERE refSeqAli.qname=gbSeq.acc</pre>. To remove the transcripts on haplotypes, add this condition at the end: <pre>and tName NOT LIKE '%_hap%' AND tName not like '%_alt%' AND tNAME NOT LIKE '%_fix%'</pre>.
+SELECT matches,misMatches,repMatches,nCount,qNumInsert,qBaseInsert,tNumInsert,tBaseInsert,strand,concat(qName, '.', gbSeq.version),qSize,qStart,qEnd,tName,tSize,tStart,tEnd,blockCount,blockSizes,qStarts,tStarts from refSeqAli, hgFixed.gbSeq WHERE refSeqAli.qname=gbSeq.acc</pre>
+<p>To remove the transcripts on haplotypes, add this condition at the end:</p>
+<pre>and tName NOT LIKE '%_hap%' AND tName not like '%_alt%' AND tNAME NOT LIKE '%_fix%'</pre>
 
 <p>A word of caution on the NCBI RefSeq track on hg19: NCBI is not fully supporting hg19 anymore. As a result, 
 some genes are not located on the main chromosomes in anymore. An example is NM_001129826/CSAG3.
 For hg19, you may prefer UCSC RefSeq for now.</p>
 <a name="mito"></a>
 <h2>What is the best gene track for mitochondrial gene annotations</h2>
 <p>
 The mitochondrial sequence included in assembly sequence files is 
 a special case and most of what has been explained on this page does not apply
 to the mitochondrial gene annotations. For most assemblies in the Genome
 Browser, the sequence name of the mitochondrial genome is "chrM".</p>
 
 <p>Both GENCODE and RefSeq databases
 import their mitochondrial gene annotation directly from the rCRS 
 RefSeq record