Index of /public/2024Q4/Vega/PureTargetCoriell24
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puretarget_report.genotype.csv 2024-11-04 09:13 37K
README.txt 2024-11-05 06:11 3.3K
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