aa048e375b37cade56f3f3f2c3a35fc16fb357a0 max Fri Jan 17 05:38:23 2020 -0800 adding NCBI Refseq Select track, refs #24787 diff --git src/hg/makeDb/doc/hg38/ncbiRefSeq.txt src/hg/makeDb/doc/hg38/ncbiRefSeq.txt index d672c48..b0d3029 100644 --- src/hg/makeDb/doc/hg38/ncbiRefSeq.txt +++ src/hg/makeDb/doc/hg38/ncbiRefSeq.txt @@ -300,15 +300,23 @@ # ncbiRefSeq 4.418%, refGene 3.098%, both 3.073%, cover 69.56%, enrich 22.45x # previous: # ncbiRefSeq 4.332%, refGene 3.098%, both 2.920%, cover 67.40%, enrich 21.75x featureBits -enrichment hg38 ncbiRefSeqCurated refGene # ncbiRefSeqCurated 3.073%, refGene 3.098%, both 3.067%, cover 99.81%, enrich 32.22x # previous: # ncbiRefSeqCurated 2.880%, refGene 3.098%, both 2.846%, cover 98.84%, enrich 31.90x featureBits -enrichment hg38 refGene ncbiRefSeqCurated # refGene 3.098%, ncbiRefSeqCurated 3.073%, both 3.067%, cover 98.99%, enrich 32.22x # previous: # refGene 3.098%, ncbiRefSeqCurated 2.880%, both 2.846%, cover 91.86%, enrich 31.90x ######################################################################### +# addition of RefSeq Select-restricted subset, Max, Feb 10 2019 +cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06/ +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 +zcat process/hg38.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp +hgLoadGenePred -genePredExt hg38 ncbiRefSeqSelect refseqSelect.curated.gp +wc -l refseqSelect.curated.gp +6378 refseqSelect.curated.gp +#############################################################################