Pipeline for RNA Sequence or Transcriptome Analysis
RNA sequencing analysis pipeline is based on current analysis systems for differential gene expression and mutation (splicing,point mutation) detection in exome. 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 transcriptome 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 quality of sequence,
for adaptor clipping, use TRIMMOMATIC
click TRIMMOMATIC or for
FASTQGROOMER,FASTQGroomer
If you have output from TRIMMOMATIC
or FASTQGROOMER and to use BWA,
click BWA or BOWTIE2
BWA or BOWTIE2 output should be
analyzed with and to use TOPHAT2
click TOPHAT2 for splcing file
and gene expression file.
Gene expression .bam files can be passed
through CUFFMERGE for control
and experimental samples
.To use CUFFMEGE, click
CUFFMERGE
CUFFMERGE output control and samples
should be passed through CUFFCOMPARE
.To use CUFFCOMPARE, click
CUFFCOMPARE
For differential gene expression of
pooled control vs experimental samples,
use CUFFDIFF. To use CUFFDIFF,
click CUFFDIFF
For viewing graphs and charts for
custom genes, use
CUMMERBUND
For analyzing with R package, a complete
different system DESEQ2 can be used!
Before using DESEQ2, you should
pass through RNAseqgene.
Click for rnaseqGene
rnaseqGene output can be
analyzed through DESEQ2 for
differentially expressed gene. Click for
DESEQ2
For Gene Set Enrichment Analysis,
use GSEA. To use GSEA click
GSEA
For pathway analysis, use IPA or
KEGG or CYTOSCOPE.To use them click
IPA or KEGG or CYTOSCOPE