aa048e375b37cade56f3f3f2c3a35fc16fb357a0
max
  Fri Jan 17 05:38:23 2020 -0800
adding NCBI Refseq Select track, refs #24787

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 4e460b2..b92b2af 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33951,15 +33951,23 @@
     #     float obs_exp;      "Observed/expected score"
     #     float chisq;       "Chi-Squared Difference"
     #     )
 
     # now we can make the bigBed:
     ./aaToGenomic.py trimmedUtrs.txt 148353-3/Table_S4.csv | sort -k1,1 -k2,2n > missenseConstrained.bed
     bedToBigBed -tab -type=bed12+5 -as=missenseBed.as missenseConstrained.bed /hive/data/genomes/hg19/chrom.sizes missenseConstrained.bb
     # pass1 - making usageList (24 chroms): 5 millis
     # pass2 - checking and writing primary data (6507 records, 17 fields): 134 millis
     # only a few genes:
     cut -f13 missenseConstrained.bed | sort | uniq | wc -l
     # 2700
     ln -s /gbdb/hg19/gnomAD/missenseConstrained.bb missenseConstrained.bb
 
 ##############################################################################
+# adding RefSeq Select to NCBIRefSeq, Max, Feb 17 2020
+cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2019-11-21
+zcat download/*_genomic.gff.gz | grep 'tag=RefSeq Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
+cat process/hg19.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp
+hgLoadGenePred -genePredExt hg19 ncbiRefSeqSelect refseqSelect.curated.gp
+wc -l refseqSelect.curated.gp
+9355 refseqSelect.curated.gp
+##############################################################################