1 Analysis of DNA mehylation of rice population
1.1 The program can be used for mapping BS-seq data with PE-reads and generate reports for QC, mapping and methylation level.
#dependents
#bowtie2-2.2.9
#bismark
#fastq
usage:perl 01_bismark_for_PE_reads.pl $ARGV[0]
1.2 Merged cytosines methylated state of each accession.
usage:perl 01_merge_bismark_CG_for_population_genetics.pl 01_CG
2 Analysis of SNPs
2.1 The program can be used for mapping re-seq data with PE-reads and generate snp.
#dependents
#bwa
#fastq
#gatk
usage:perl 02_reseq_generate_SNPs_for_PE_reads.pl $ARGV[0]
2.2 merged GenotypeGVCFs
gatk --java-options -Xmx60g CombineGVCFs -V line1.g.vcf -V line1.g.vcf -R ../genome -O 01_CombineGVCFs_out.vcf
gatk --java-options -Xmx60g GenotypeGVCFs -R ../genome -V 01_CombineGVCFs_out.vcf -O 01_GenotypeGVCFs_out.vcf
2.3 SplitVcfs
gatk SelectVariants -R ../genome -select-type SNP -V 01_GenotypeGVCFs_out.vcf -O 02_GenotypeGVCFs_out.snp.vcf
2.4 filt SNP
gatk VariantFiltration -R ../genome -V 02_GenotypeGVCFs_out.snp.vcf -O 02_VariantFiltration.snp.vcf --filter-expression "QD < 10.0 || MQ < 50.0 || FS > 30.0 || SOR > 3.0 || MQRankSum < -2.5 || ReadPosRankSum < -3.5 || DP<2.0 ||DP>100.0" --filter-name "Fail" -G-filter "DP<2 || isHet==1 || isHomRef==1" -G-filter-name "Failed" &
#and then selected filter SNPs
2.5 conversion using Plink
plink --vcf 02_VariantFiltration_select.snp.vcf --recode vcf-iid --out 03_select.snp --allow-extra-chr
2.6 conversion to phy
python vcf2phylip.py --input 03_select.snp.vcf
2.7 Phylogeny Reconstruction of Neighbor-joining
/DATA2/maize2/21_software/MegaX/megacc -a infer_NJ_nucleotide.mao -d 03_select.snp.meg -o 03_select.snp.recode
2.8 Nucleotide diversity (p)was
vcftools --vcf 03_select.snp.vcf --keep wild.txt --recode --recode-INFO-all --out wild
vcftools --vcf wild.recode.vcf --out wild --window-pi 100000 --window-pi-step 10000
paste wild.windowed.pi.txt aro.pi.txt aus.pi.txt geng.pi.txt indica.pi.txt weedyin.pi.txt weedyge.pi.txt >all_line.pi.txt
3 RNA-seq analysis
3.1 split each rnaseq data based on the indexs
python split_fastq_for_each_tissue.py $R1 $R2 index.txt
3.2The program can be used for mapping 3RNA-seq data with single-reads and generate gene expression level.
#dependents
#bowtie2-2.2.9
#hisat2
#fastq
usage:perl 03_RNA-seq_for_gene_expression.pl $ARGV[0]
4 DAP-seq analysis
4.1 The program can be used for mapping DAP-seq with PE-reads and generate reports for QC, mapping and IGV.
#dependents
#fastq
#bwa
#samtools
#igvtools
usage:perl 04_DAP-seq_with_PE_reads_mapping.pl $ARGV[0]
4.2 The program can be used for peaks-calling.
#dependents
#MACS2.1.2
#gem
#bedtools
#meme
usage:perl 04_DAP-seq_with_PE_reads_callpeaks_under_control.pl $ARGV[0] $ARGV[1]
5 ATAC-seq analysis
5.1 The program can be used for mapping ATAC-seq with PE-reads and generate reports for QC, mapping and IGV.
#dependents
#fastq
#bwa
#samtools
#igvtools
usage:perl 05_ATAC-seq_for_PE_reads_mapping.pl $ARGV[0]
5.2 The program can be used for peaks-calling.
#dependents
#MACS2.1.2
#bedtools
#meme
usage:perl 05_DAP-seq_with_PE_reads_callpeaks_under_nakedDNA.pl $ARGV[0] $ARGV[1]