Tools_to_analysis_DNA_seq&Epigenetic_Data.md

2) DNA-seq

(2.1) Mapping and QC

• Remove adaptor: cutadapt, Trimmomatic
• Mapping: Bowtie2, STAR
• QC: fastqc

(2.2) Mutation

• Mutation discovery: GATK, Varscan
• Mutation annotation: ANNOVAR

(2.3) Assembly

• denovo assembly software: Trinity

(2.4) CNV

• Whole Genome Seq: Control-FREEC
• Whole exome Seq: CONTRA, ExomeCNV

(2.5) SV (structural variation)

• Breakdancer

5) Epigenetic Data

(5.1)DNA Methylation

• Bi-sulfate data:
  • Review: Katarzyna Wreczycka, et al. Strategies for analyzing bisulfite sequencing data. Journal of Biotechnology. 2017.
  • Mapping: Bismark, BSMAP
  • Differential Methylation Regions (DMRs) detection: methylkit, ComMet
  • Segmentation of the methylome, Classification of Fully Methylated Regions (FMRs), Unmethylated Regions (UMRs) and Low-Methylated Regions (LMRs): MethylSeekR
  • Annotation of DMRs: genomation, ChIPpeakAnno
  • Web-based service: WBSA
• IP data:
  • Overview to CHIP-Seq: https://github.com/crazyhottommy/ChIP-seq-analysis
  • peak calling: MACS2
  • Peak annotation: HOMER annotatePeak, ChIPseeker
  • Gene set enrichment analysis for ChIP-seq peaks: GREAT

(5.2)DNAase-seq:

• review : Yongjing Liu, et al. Brief in Bioinformatics, 2019.
• peek calling: F-Seq
• peek annotation: ChIPpeakAnno
• Motif analysis: MEME-ChIP

(5.3)ATAC-seq:

• pipeline recommended by Harward informatics
• peek calling: MACS2
• peak annotation: ChIPseeker
• Motif discovery: HOMER