Pipeline for ATAC Sequence Analysis

ATAC sequencing is used to map the transcription factor binding site (transposon insertion sites) and is based on current analysis systems. Raw sequences as FASTQ files that come from NGS sequencer (e.g. ILLUMINA Miseq, Hiseq, Novaseq; Perkin Elmer, ION torrent) should be analyzed through a series of software to detect variants. A pipeline for Exome sequence analysis is given with resepective software to use step-by-step.


If You have raw .fastq sequence from a
sequencer and wish to upload .fastq file,
click
upload





If you wish to use FASTQC with
or without uploading .fastq files,clic
FASTQC





After seeing sequencing quality report,
and to use TRIMMOMATIC,
click TRIMMOMATIC or to use
FASTQGROOMER, click
FASTQGROOMER



If you have output from TRIMMOMATIC
or FASTQGROOMER and to use BWA
click
BWA








If you have BWA output and to use
MACS
clic
MACS or click SICER

SICER





To map and view the binding region
,use IGV IGV or NEBULA NEBULA