5148aa7d55ecbad1137ae3cd4bb0c85b67e8fed3
markd
  Thu Apr 14 12:13:05 2022 -0700
added cat/liftoff rna and protein fastas

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 349b2da..912718c 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -93,30 +93,40 @@
 catLiftOffGenesV1 (2022-03-15 markd)
 ----------------------------------------------------------------
 from Marina Haukness <mhauknes@ucsc.edu>
 
 http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.bb
 http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3
 
 rename to
   catLiftOffGenesV1.bb
   catLiftOffGenesV1.gff3.gz
 
 # create GTF
   zcat catLiftOffGenesV1.gff3.gz | gffread /dev/stdin -T -o catLiftOffGenesV1.gtf
   pigz catLiftOffGenesV1.gtf 
 
+
+# obtain sequence fastas
+   http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.fasta
+   http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.protein.fasta
+
+   mv CHM13.v2.0.fasta catLiftOffGenesV1.rna.fa
+   mv CHM13.v2.0.protein.fasta  catLiftOffGenesV1.protein.fa
+   pigz *.fa
+   
+
 ================================================================
 * hgLiftOver (2022-03-26 markd)
 ----------------------------------------------------------------
 GRCh38 & GRCh37 Nae-Chyun Chen <naechyun.chen@gmail.com>
 
 # 2022-04-09 it was noted that chrM was left out of above alignments, so obtain them and repeat
 
 globus: /team-liftover/v1_nflo/with_chrM/
     chm13v2-grch38.chain
     grch38-chm13v2.chain
     chm13v2-hg19_chrM.chain
     chm13v2-hg19_chrMT.chain
     hg19_chrM-chm13v2.chain
     hg19_chrMT-chm13v2.chain
 
@@ -173,33 +183,36 @@
 
    http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/t2tChm13.v2.0.hal
 
 # rename genomes to match browser, in renameFile.tab put
 GRCh38	hg38
 CHM13	GCA_009914755.4
 
     halRenameGenomes t2tChm13.v2.0.hal renameFile.tab 
 
 # NOTE: disabled due to Snakes not using chromAlias
 
 ================================================================
 * hgUnique (2022-03-30 markd)
 ----------------------------------------------------------------
 regions not in hg38:
+original version in:
 globus: /team-liftover/v1_nflo/T2T-CHM13v2.0_new_and_non_syntenic_regions.bed
          chm13v2-unique_to_hg19.bed
          chm13v2-unique_to_hg38.bed
+however, with the addition of 
+
 
 #
 chainToPslBasic ../hgLiftOver/chm13v2-hg38.over.chain.gz stdout \
   | pslToBed stdin stdout \
   | bedtools sort -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \
   | bedtools merge \
   | bedtools complement -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \
   | bedtools merge \
   | sort -k1,1 -k2,2n \
   > chm13v2-unique_to_hg38.bed
 
 chainToPslBasic ../hgLiftOver/chm13v2-hg19.over.chain.gz stdout \
   | pslToBed stdin stdout \
   | bedtools sort -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \
   | bedtools merge \