OVERVIEW
  PacBio files for the PureTarget repeat expansion panel
  Data are Coriell cell lines sequenced on Vega
  Due to restrictions on sharing of Personally Identifying Genetic Information (PIGI)
  	sequence data is available only for the target of interest for each sample. TRGT plots,
  	genotypes, and read depth stats are available for the 20 gene panel.


METHODS
	LIBRARY PREPARATION AND REAGENTS
  		Library constructed according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Generating-PureTarget-repeat-expansion-panel-libraries.pdf
  		DNA samples were treated with DNA repair enzymes prior to library prep using a pre-release protocol
  		2 ug of DNA used per sample, except C9orf72 samples ND11494 and ND14442 (640ng each)
  		PureTarget repeat expansions panel - PacBio 103-390-400
  		SMRTbell® adapter index plate 96A (for barcoding) - PacBio 102-009-200
	SEQUENCING
  		Vega, 24 hr movie, PureTarget repeat expansion application run design.
  		Movie context m21007_240927_225820
	ANALYSIS
		Analysis with SMRT Link 25.1.0.253645


DIRECTORIES
PBMM2-BAM-Input-For-IGV-And-TRGT        Mapped BAM files for IGV visualization and inputs for TRGT
TRGT-BAM_Input_For_TRVZ			BAM files produced by TRGT
TRGT-VCF_files                          VCF files produced by TRGT
TRGT_plots_meth_allele       		Methylation SVG plots per allele for all 20 loci
TRGT_plots_meth_waterfall    		Methylation waterfall SVG plots for all 20 loci
TRGT_plots_motifs_allele     		Motif unit SVG plots per allele for all 20 loci
TRGT_plots_motifs_waterfall  		Motif unit waterfall SVG plots for all 20 loci


FILES DESCRIPTION
PBMM2-BAM-Input-For-IGV-And-TRGT/[SAMPLE_ID].mapped.bam						Mapped BAM file
PBMM2-BAM-Input-For-IGV-And-TRGT/[SAMPLE_ID].mapped.bam.bai					Mapped BAM file index
TRGT-BAM_Input_For_TRVZ/[SAMPLE_ID].[EXPANDED_LOCUS].trgt.spanning.bam				TRGT BAM output
TRGT-BAM_Input_For_TRVZ/[SAMPLE_ID].[EXPANDED_LOCUS].trgt.spanning.bam.bai			TRGT BAM index
TRGT-VCF_files/[SAMPLE].trgt.vcf								TRGT VCF output
TRGT-plots_meth_allele/[SAMPLE_ID]_meth_allele.trvz_alleles/[LOCUS].trvz.svg			Locus SVG image
TRGT-plots_meth_waterfall/[SAMPLE_ID]_meth_waterfall.trvz_alleles/[LOCUS].trvz.svg		Locus SVG image
TRGT-plots_motifs_allele/[SAMPLE_ID]_motifs_allele.trvz_alleles/[LOCUS].trvz.svg		Locus SVG image
TRGT-plots_motifs_waterfall/[SAMPLE_ID]_motifs_waterfall.trvz_alleles/[LOCUS].trvz.svg		Locus SVG image
puretarget_report.genotype.csv									Genotype table with per-allele coverages and lengths (see SMRT Link v13.1 User Guide for details)

SAMPLES
Samples obtained from https://www.coriell.org/
SAMPLE_ID	CORIELL_ID	EXPANDED_LOCUS	KARYOTYPE
HG01175-RFC1	HG01175	RFC1	XX
HG04228-RFC1	HG04228	RFC1	XY
HM03756-DMPK	HM03756	DMPK	XY
HM06968-FMR1	HM06968	FMR1	XX
HM16212-FXN	HM16212	FXN	XX
HM23629-PABPN1	HM23629	PABPN1	XX
HM23709-AR	HM23709	AR	XY
NA03697-DMPK	NA03697	DMPK	XY
NA06153-ATXN3	NA06153	ATXN3	XY
NA06905-FMR1	NA06905	FMR1	XX
NA09237_rep1-FMR1	NA09237	FMR1	XY
NA09237_rep2-FMR1	NA09237	FMR1	XY
NA13509-HTT	NA13509	HTT	XX
NA13515-HTT	NA13515	HTT	XY
NA13536-ATXN1	NA13536	ATXN1	XX
NA13716-ATN1	NA13716	ATN1	XY
NA15850-FXN	NA15850	FXN	XY
NA16202-FXN	NA16202	FXN	XX
NA16212-FXN	NA16212	FXN	XX
NA16215-FXN	NA16215	FXN	XX
NA16237-FXN	NA16237	FXN	XX
NA20752-RFC1	NA20752	RFC1	XY
ND11494-C9ORF72	ND11494	C9ORF72	XY
ND14442-C9ORF72	ND14442	C9ORF72	XY