Circompara2

Introduction

CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods.

For more information, please check:
Home page: https://github.com/egaffo/circompara2

Versions

  • 0.1.2.1

Commands

  • python

  • Rscript

  • circompara2

  • CIRCexplorer2

  • CIRCexplorer_compare.R

  • CIRI.pl

  • DCC

  • DCC_patch_CombineCounts.py

  • QRE_finder.py

  • STAR

  • bedtools

  • bowtie

  • bowtie-build

  • bowtie-inspect

  • bowtie2

  • bowtie2-build

  • bowtie2-inspect

  • bwa

  • ccp_circrna_expression.R

  • cfinder_compare.R

  • chimoutjunc_to_bed.py

  • ciri_compare.R

  • collect_read_stats.R

  • convert_circrna_collect_tables.py

  • cuffcompare

  • cuffdiff

  • cufflinks

  • cuffmerge

  • cuffnorm

  • cuffquant

  • dcc_compare.R

  • dcc_fix_strand.R

  • fasta_len.py

  • fastq_rev_comp.py

  • fastqc

  • filterCirc.awk

  • filterSpliceSiteCircles.pl

  • filter_and_cast_circexp.R

  • filter_fastq_reads.py

  • filter_findcirc_res.R

  • filter_segemehl.R

  • find_circ.py

  • findcirc_compare.R

  • gene_annotation.R

  • get_ce2_bwa_bks_reads.R

  • get_ce2_bwa_circ_reads.py

  • get_ce2_segemehl_bks_reads.R

  • get_ce2_star_bks_reads.R

  • get_ce2_th_bks_reads.R

  • get_circompara_counts.R

  • get_circrnaFinder_bks_reads.R

  • get_ciri_bks_reads.R

  • get_dcc_bks_reads.R

  • get_findcirc_bks_reads.R

  • get_gene_expression_files.R

  • get_stringtie_rawcounts.R

  • gffread

  • gtfToGenePred

  • gtf_collapse_features.py

  • gtf_to_sam

  • haarz.x

  • hisat2

  • hisat2-build

  • htseq-count

  • install_R_libs.R

  • nrForwardSplicedReads.pl

  • parallel

  • pip

  • postProcessStarAlignment.pl

  • samtools

  • samtools_v0

  • scons

  • segemehl.x

  • split_start_end_gtf.py

  • starCirclesToBed.pl

  • stringtie

  • testrealign_compare.R

  • tophat2

  • trim_read_header.py

  • trimmomatic-0.39.jar

  • unmapped2anchors.py

  • cf_filterChimout.awk

  • circompara

  • get_unmapped_reads_from_bam.sh

  • install_circompara

  • make_circrna_html

  • make_indexes

Module

You can load the modules by:

module load biocontainers
module load circompara2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run circompara2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=circompara2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers circompara2