Index of /public/dataset/PureTargetRE/RFC1

Icon  Name                              Last modified      Size  Description
[PARENTDIR] Parent Directory                                       -   
[DIR] TRVZ-RFC1_plots_motifs_waterfall/ 2024-04-15 16:25    -   
[DIR] TRVZ-RFC1_plots_motifs_allele/    2024-04-08 14:13    -   
[DIR] TRGT-VCF_files/                   2024-04-08 14:25    -   
[DIR] TRGT-BAM_Input_For_TRVZ/          2024-04-08 14:25    -   
[DIR] PBMM2-BAM-Input-For-IGV-And-TRGT/ 2024-04-08 14:25    -   
[TXT] README.txt                        2024-04-12 16:19  2.8K  
[TXT] QC-Target_Genotype_Table.csv      2024-04-08 14:24  1.1K  

OVERVIEW
  PacBio files for the PureTarget repeat expansion panel
  Data are samples with RFC1 expansions sequenced on a Sequel IIe
  Sample provided by Prof Georgia Karadima & Prof Georgios Koutsis, Neurogenetics Unit, 1st Department of Neurology, Eginition Hospital, NKUA

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 RFC1
TRVZ-all_target_plots_meth_waterfall    Methylation waterfall SVG plots from TRVZ for RFC1
TRVZ-all_target_plots_motifs_allele     Motif unit SVG plots per allele from TRVZ for RFC1
TRVZ-all_target_plots_motifs_waterfall  Motif unit waterfall SVG plots from TRVZ for RFC1

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.bam               Mapped BAM file
PBMM2-BAM-Input-For-IGV-And-TRGT/[SAMPLE].pbmm2.bam.bai           Mapped BAM file index
QC-Target_Genotype_Table.csv                                      Genotype table with per-allele RFC1 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].trvz.svg               Locus SVG image (TRVZ meth/allele output)
TRVZ-all_target_plots_meth_waterfall/[SAMPLE].trvz.svg            Locus SVG image (TRVZ meth/waterfall output)
TRVZ-all_target_plots_motifs_allele/[SAMPLE].trvz.svg            Locus SVG image (TRVZ motifs/allele output)
TRVZ-all_target_plots_motifs_waterfall/[SAMPLE].trvz.svg          Locus SVG image (TRVZ motifs/waterfall output)

SAMPLES EXPECTED_GENOTYPE
  NG5   2A3Gexp/2A3Gexp
  NG10  2A3G(x11)/4A1G-3A2Gexp
  NG11  4A1G(x11)/3A2G-2A3Gexp
  NG24  2A3Gexp/2A3Gexp
  NG26  2A3Gexp/2A3Gexp

Expected genotypes: sizing by PCR and the 3 RP-PCRs as described in Cortese et al 2019 (doi:10.1038/s41588-019-0372-4).