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

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

0.1.2.1

BELL

0.1.2.1

GAUTSCHI

0.1.2.1

NEGISHI

0.1.2.1

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers circompara2

# Your circompara2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers circompara2

# Your circompara2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers circompara2

# Your circompara2 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers circompara2

# Your circompara2 workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers circompara2

# Your circompara2 workflow...