3f76453673b9825c8057d3f16f2c4dd12800daab
braney
  Tue Sep 13 14:25:13 2022 -0700
added PCR amplicon track to mpxvRivers

diff --git src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt
new file mode 100644
index 0000000..e30e1b2
--- /dev/null
+++ src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt
@@ -0,0 +1,19 @@
+mkdir /hive/data/genomes/mpxvRivers/bed/pcrAmplicon
+cd /hive/data/genomes/mpxvRivers/bed/pcrAmplicon
+
+# grab this file:     https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-5qpvob1nbl4o/v2/materials/MPXV-primer_genome-positions.tsv
+
+dos2unix MPXV-primer_genome-positions.tsv
+
+# convert left and right primers on separate lines to the one line formation isPcr expects
+grep LEFT MPXV-primer_genome-positions.tsv > left
+grep RIGHT MPXV-primer_genome-positions.tsv > right
+paste left right | tawk '{print $1, $3, $12}' > query.txt
+
+# do the isPcr
+isPcr ../../mpxvRivers.2bit query.txt ispcr.out
+
+# convert isPcr fasta output to bed12 with left and right as two "exons" plus two extra fields with sequence in them
+grep ">" ispcr.out | tr -d '>' | tr ':' ' ' | awk '/+/ {strand="PS"} /-/ {strand="MS"} {print $1, $2, $3, strand, $4,$5,$6}' | tr '-' ' ' | tr '+' ' ' | sed 's/bp//' | awk '{$2=$2-1;print $1, $2, $3, $4, 0, $5, $2,$3, "0,0,0", 2, length($7) "," length($8), 0 "," $3 - length($8) - $2,$7,$8}' | sed 's/MS/-/' | sed 's/PS/+/' | sed 's/_LEFT//' | sort -k1,1 -k2,2n > pcrAmplicon.bed
+
+bedToBigBed pcrAmplicon.bed ../../chrom.sizes pcrAmplicon.bb -as=pcrAmplicon.as -type=bed12+2