fastqc <seq1.fastq seq2.fastq ... seqN.fastq>
multiqc </path/to/*_fastqc.zip>
bowtie2-build </path/to/genome/fasta> \
</path/to/bowtie2IndexDir>
bowtie2 -p <NumberOfThreads> \
-q \
--local \
-x </path/to/bowtie2IndexDir> \
-U </path/to/fastq> \
-S </path/to/align.sam>
samtools view -h -S -b \
--threads <NumberOfThreads> \
-o </path/to/align.bam> \
</path/to/align.sam>
sambamba sort -t <NumberOfThreads> \
-o </path/to/align.sorted.bam> \
</path/to/align.bam>
sambamba view -h \
-t <NumberOfThreads> \
-f bam \
-F "[XS] == null and not unmapped " \
</path/to/align.sorted.bam> \
> </path/to/align.sorted_filtered.bam>
macs3 callpeak -t </path/to/chip.bam> \
-c </path/to/input.bam> \
-f BAM \
-g <genome_sized> \
-q <qvalue_cutoff> \
-n </path/to/output/dir/prefix> \
--outdir </path/to/output/dir>
macs3 callpeak --broad \
-t </path/to/chip.bam> \
-c </path/to/input.bam> \
-f BAM \
-g <genome_sized> \
--broad-cutoff <broad_region_cutoff> \
-n </path/to/output/dir/prefix> \
--outdir </path/to/output/dir>
#R code
library(DiffBind)
dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE)
dbObj_contrast <- dba.contrast(dbObj, categories=DBA_FACTOR, minMembers = 2)
dbObj_contrast_analyze <- dba.analyze(dbObj_contrast)
dba.plotPCA(dbObj_contrast_analyze, contrast=1, method=DBA_ALL_METHODS, attributes=DBA_FACTOR, label=DBA_ID)