Index of /public/dataset/HiFiTE_SqIIe/Oct_2022/TwistAllianceDarkGene

Icon  Name                                                         Last modified      Size  Description
[PARENTDIR] Parent Directory - [   ] NA12878.fastq.gz 2022-10-17 14:34 2.6G [   ] NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam 2022-10-17 08:15 2.1G [   ] NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam.bai 2022-10-17 08:15 2.1M [TXT] README.txt 2022-11-11 12:02 1.2K [TXT] TwistAllianceDarkGenes_GeneList.txt 2022-11-11 11:47 2.3K [   ] human_GRCh38_no_alt_analysis_set.fasta 2022-10-17 08:25 2.9G
	PacBio HiFi reads for NA12878 from target enrichment Twist Alliance Dark Gene Panel.
	1 of 4 samples sequenced on Sequel IIe SMRT Cell 8M released here.

	SHEARING	Covaris g-TUBE to target size of 8kb.
	TWIST LIBRARY	Prepared according to
			Probes: Twist Alliance Dark Genes Panel
	PACBIO LIBRARY 	Prepared according to
	SEQUENCING	Sequel IIe System, 24 hr movie, Sequel II Chemistry 2.0, Binding Kit 3.2
	ANALYSIS	Generate HiFi reads with ccs v6.3.0
			Demultiplex with lima v2.5.0
			Mark PCR Duplicates with pbmarkdups v1.0.2
			Align to GRCh38_no_alt_analysis_set with pbmm2 v1.7.0
			Call variants with pbsv v2.8 and DeepVariant v1.4.0
			Phase with whatshap 1.1

NA12878_B11_2ul.GRCh38_noalt.deepvariant.haplotagged.bam	aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag)
NA12878.fastq.gz						demultiplexed HiFi reads
human_GRCh38_no_alt_analysis_set.fasta				reference used to generate BAM files
TwistAllianceDarkGenes_GeneList.txt				gene list