e68b8a55273a3b04eb0560a2a40115540ce1dca0
gperez2
  Tue Jan 23 14:28:04 2024 -0800
Making the Affy CytoScan HD track for hg38, refs #32856

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 7c66c23..90d487c 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -7257,15 +7257,33 @@
 | phenDis    | Phenotype and Literature           |      3.4 |               0 |
 | pub        | Literature                         |      3.5 |               0 |
 | hprc       | Human Pangenome - HPRC             |      3.6 |               0 |
 | covid      | COVID-19                           |      3.6 |               0 |
 | singleCell | Single Cell RNA-seq                |      3.7 |               0 |
 | rna        | mRNA and EST                       |        4 |               0 |
 | expression | Expression                         |      4.5 |               0 |
 | regulation | Regulation                         |        5 |               0 |
 | compGeno   | Comparative Genomics               |        6 |               0 |
 | varRep     | Variation                          |        7 |               0 |
 | rep        | Repeats                            |        8 |               0 |
 | x          | Experimental                       |       10 |               1 |
 +------------+------------------------------------+----------+-----------------+
 
 ##############################################################################
+# Affy CytoScan HD track, refs #32856  (2024-01-23 Gerardo)
+cd /hive/data/genomes/hg38/bed/
+mkdir genotypeArrays; cd genotypeArrays
+#The user sent Gerardo a direct email with a shared folder link. Gerardo downloaded the bed files and made them available on dev.
+#The user provided two bed files (https://hgwdev-gperez2.gi.ucsc.edu/~gperez2/mlq/mlq_32791/). Gerardo used the version 2 bed file for the track.
+wget https://hgwdev-gperez2.gi.ucsc.edu/~gperez2/mlq/mlq_32791/CytoScanHD_Accel_Array.na36.bed.zip
+unzip CytoScanHD_Accel_Array.na36.bed.zip
+# Removed header and sorted the file
+grep -v 'track' CytoScanHD_Accel_Array.na36.bed | bedSort stdin stdout > affyCytoScanHD.bed
+bedToBigBed -tab -type=bed12 affyCytoScanHD.bed https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes affyCytoScanHD.bb 
+cd /gbdb/hg38
+mkdir genotypeArrays; cd genotypeArrays
+# Making symlink for big file and raw bed file
+ln -s /hive/data/genomes/hg38/bed/genotypeArrays/affyCytoScanHD.bb
+ln -s /hive/data/genomes/hg38/bed/genotypeArrays/CytoScanHD_Accel_Array.na36.bed.zip
+cd ~/kent/src/hg/makeDb/trackDb/human/hg38
+vi trackDb.ra
+##############################################################################