Pipeline for bisulfite DNA Sequence Analysis
BIsulfite modified DNA sequencing analysis is based on current analysis systems for identifying methylated cytosine and their percentage of occurance in the cell. 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,click
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
METHYLSEQ
click METHYLSEQ or click BISMARK
BISMARK
To map and view the binding region use IGV
IGV or METHYLATION MAPPER,
METHYLATION MAPPER