
July 2023

===============================================================================


The Perl script in this directory will classify ONT reads mapped to the chr4qA,
chr4qB, and chr10 D4Z4 regions.

An input BAM file of ONT reads is required that was generated using minimap2.
The reference genome should be T2T CHM13v2.0/hs1 that includes the chr4qB
HG002-1-JAHKSE010000016_1-200000_rev.fasta contig. A fasta file for that contig
(a 200kb contig with a 4qB D4Z4 array) is included in this directory to
build the appropriate minimap2 index.

This Perl script requires the cross_match program written by Brent Ewing,
Phil Green, and David Gordon at the University of Washington.
http://www.phrap.org/consed/consed.html#howToGet.

This Perl script also requires samtools.

The DATA_FILES sub-directory includes required fasta files.

An example BAM file is included to test the required executables.

Run example =

./Assign_D4Z4_Reads.pl -f Test_D4Z4-targeted-reads_SUP_5mC_chm13v2.0_HG002-1-JAHKSE010000016.sort.bam -d Output_Test_D4Z4-reads -o Output_Test_D4Z4-targeted-reads


================================================================================

Bob Weiss
bob.weiss@genetics.utah.edu

