FAQs / Resources

Administration

1. How do I get started working with the NGS services? (User Manual)
2. How do I fill out the forms on NGS Core LIMS?
3. How do I download my sequencing data?
4. How do I pay my fees? (Billing Procedures)
5. 《客製化需求同意書》

Experiment Related

1. How to select index for illumina sequencing?
2. Index hopping issue on patterned flowcells and methods of mitigation. (NextSeq2000 / iSeq)
3. Commonly used Illumina library prep kits and protocols.
4. Illumina Adapter Sequences
   v1, Nextera UD Indexes (p.24)
   v2, IDT for Illumina UD Indexes
   v3, Illumina Unique Dual Indexes
5. RNA-seq data processing: HTSream and FASTP
   
   Why does FASTQC show unexpectedly high sequence duplication levels (PCR-duplicates)?
   (From UC Davis Genome Center)
6. Adaptor trimming for TruSeq DNA Methylation
7. Illumina PhiX control is GI:9626372 RefSeq:NC_001422.
8. Amplicon-seq design for Illumina library architecture
9. Illumina Chemistry and imaging

Sequencing Platform

Illumina Document

PacBio Document

PacBio Data Revio

Oxford Nanopore Document

Illumina Knowledge

SMRTlink　　User Guide

Workflow in SMRTlink

Nanopore EPI2ME Workflows

PacBio pbbioconda

Nanopore Tutorial

PacBio lima (Demultiplexer)

PacBio IsoSeq　(De Novo Isoform)

Hifiasm (De Nove Assembler)

Single-cell ＆ Spatial analyses

10x Genomics　　Support

10x Genomics　　Document

10x Genomics　　Software

Illumina Partek Ebook

Illumina Partek Document

PacBio Spatial Webinar

10x Genomics　Loupe Browser

10x Genomics　　Loupe V(D)J Browser

3D Genomes

3D Genomes Reference

Dovetail　　User Guides

Phase　Genomics

Arima　　Genomics

Nature　　　　　　　　　　The 3D Genome Reference

Dovetail　　Omni-C Doc

Northwestern University　　　　YUE Lab (genomics/epigenomics)

Dovetail　　Micro-C Doc

YaHS　　　　　　　　　 (Hi-C scaffolding tool)