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CIRCexplorer2 (version 2.3.8+galaxy0)

Tool module:

CIRCexplorer2 contains 5 modules. Each module functions as an independent component owning its distinctive duty. Meanwhile, they inteact with each other, and different circular RNA analysis pipelines are derived from different combinations of several modules.

Annotation GTF file:

Reference genome:

In FASTA format

RNA-seq FASTQ file(s):

Only single-read RNA-seq is supported. It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment

Create BigWig file:

It will not consider strand information of read alignment

Scale BigWig to HPB:

Expression levels will be scaled to hits per billion-mapped-bases (HPB)

Skip TopHat mapping:

CIRexplorer2 aligns reads onto genome and transcriptome using TopHat2 to reduce false positive reads aligned in the TopHat-Fusion alignment step

Skip TopHat fusion:

It is useful for poly(A)+ RNA-seq

Purpose

CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.

Features

Precisely annotate circular RNAs (Annotate)

Support multiple circular RNA aligners (TopHat2/TopHat-Fusion, STAR, MapSplice, BWA and segemehl) (Align and Parse)

De novo assemble novel circular RNA transcripts (Assemble)

Characterize various of alternative (back-)splicing events of circular RNAs (Denovo)

Fast identify circuar RNAs with STAR or BWA (Parse)

Support both single-read and paired-end sequencing.

Modules

CIRCexplorer2 documentation is available from here, including installation instructions and tutorial.