Index of /public/dataset/PureTargetRE/Coriell

Icon  Name                                    Last modified      Size  Description
[PARENTDIR] Parent Directory                                             -   
[DIR] TRVZ-all_target_plots_motifs_waterfall/ 2024-03-29 14:22    -   
[DIR] TRVZ-all_target_plots_motifs_allele/    2024-03-29 14:25    -   
[DIR] TRVZ-all_target_plots_meth_waterfall/   2024-03-29 14:28    -   
[DIR] TRVZ-all_target_plots_meth_allele/      2024-03-29 14:31    -   
[DIR] TRGT-VCF_files/                         2024-03-11 11:19    -   
[DIR] TRGT-BAM_Input_For_TRVZ/                2024-03-11 11:20    -   
[DIR] PBMM2-BAM-Input-For-IGV-And-TRGT/       2024-03-11 11:26    -   
[TXT] README.txt                              2024-03-11 15:21  3.0K  
[TXT] QC-Target_Genotype_Table.csv            2024-03-11 11:29   11K  

OVERVIEW
  PacBio files for the PureTarget repeat expansion panel
  Data are Coriell cell lines sequenced on a Sequel IIe

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
TRVZ-all_target_plots_meth_allele       Methylation SVG plots per allele from TRVZ for all 20 loci
TRVZ-all_target_plots_meth_waterfall    Methylation waterfall SVG plots from TRVZ for all 20 loci
TRVZ-all_target_plots_motifs_allele     Motif unit SVG plots per allele from TRVZ for all 20 loci
TRVZ-all_target_plots_motifs_waterfall  Motif unit waterfall SVG plots from TRVZ for all 20 loci

METHODS
  LIBRARY PREPARATION
  		Library constructed according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Generating-PureTarget-repeat-expansion-panel-libraries.pdf
  		PureTarget repeat expansions panel; - PacBio 103-390-400
  		SMRTbell® adapter index plate 96A (for barcoding); PacBio 102-009-200
  SEQUENCING  Sequel IIe, 30 hr movie, PureTarget repeat expansion application.
  ANALYSIS
      - Demultiplex with lima v2.9.0
      - Align to GRCh38_no_alt_analysis_set with pbmm2 v1.13.1
      - Genotype with TRGT v0.8.0
      - Generate SVG plots with TRVZ v0.8.0
      - Generate CSV table with PureTarget QC v0.1.0

FILES DESCRIPTION
PBMM2-BAM-Input-For-IGV-And-TRGT/[SAMPLE].pbmm2.repeats.bam       Mapped BAM file
PBMM2-BAM-Input-For-IGV-And-TRGT/[SAMPLE].pbmm2.repeats.bam.bai   Mapped BAM file index
QC-Target_Genotype_Table.csv                                      Genotype table with per-allele coverages and lengths
TRGT-BAM_Input_For_TRVZ/[SAMPLE].trgt.spanning.bam                TRGT BAM output
TRGT-BAM_Input_For_TRVZ/[SAMPLE].trgt.spanning.bam.bai            TRGT BAM index
TRGT-VCF_files/[SAMPLE].trgt.vcf                                  TRGT VCF output
TRVZ-all_target_plots_meth_allele/[SAMPLE]-[LOCUS].svg            Locus SVG image (TRVZ meth/allele output)
TRVZ-all_target_plots_meth_waterfall/[SAMPLE]-[LOCUS].svg         Locus SVG image (TRVZ meth/waterfall output)
TRVZ-all_target_plots_motifs_allele/[SAMPLE]-[LOCUS].svg          Locus SVG image (TRVZ motifs/allele output)
TRVZ-all_target_plots_motifs_waterfall/[SAMPLE]-[LOCUS].svg       Locus SVG image (TRVZ motifs/waterfall output)

SAMPLES
Samples obtained from https://www.coriell.org/
  SAMPLE    LOCUS   CORIELL ID
  NA237092	AR      NA23709 
	NA137164	ATN1    NA13716
	NA137171	ATN1    NA13717
	NA06926A4	ATXN1   NA06926
	NA135364	ATXN1   NA13536
	NA13537A5	ATXN1   NA13537
	NA06153B4	ATXN3   NA06153
	NA03697B2	DMPK    NA03697
	NA037562	DMPK    NA03756
	NA232652	DMPK    NA23265
	NA233782	DMPK    NA23378
	NA04026C1	FMR1    NA04026
	NA05131A2	FMR1    NA05131
	NA06905A9	FMR1    NA06905
	NA09237E2	FMR1    NA09237
	NA145196	FXN     NA14519
	NA15850L1	FXN     NA15850
	NA16215B2	FXN     NA16215
	NA13509A2	HTT     NA13509
	NA135152	HTT     NA13515
	NA236291	PABPN1  NA23629