Index of /public/dataset/PureTargetRE/RFC1
Name Last modified Size Description
Parent Directory -
PBMM2-BAM-Input-For-IGV-And-TRGT/ 2024-04-08 14:25 -
TRGT-BAM_Input_For_TRVZ/ 2024-04-08 14:25 -
TRGT-VCF_files/ 2024-04-08 14:25 -
TRVZ-RFC1_plots_motifs_allele/ 2024-04-08 14:13 -
TRVZ-RFC1_plots_motifs_waterfall/ 2024-04-15 16:25 -
QC-Target_Genotype_Table.csv 2024-04-08 14:24 1.1K
README.txt 2024-04-12 16:19 2.8K
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).