Rseqc

Introduction

Rseqc is a package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/rseqc
Home page: http://rseqc.sourceforge.net

Note

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

Versions

Cluster

Version(s)

ANVIL

4.0.0

BELL

4.0.0

GAUTSCHI

4.0.0

NEGISHI

4.0.0

SCHOLAR

4.0.0

Commands

  • FPKM-UQ.py

  • FPKM_count.py

  • RNA_fragment_size.py

  • RPKM_saturation.py

  • aggregate_scores_in_intervals.py

  • align_print_template.py

  • axt_extract_ranges.py

  • axt_to_fasta.py

  • axt_to_lav.py

  • axt_to_maf.py

  • bam2fq.py

  • bam2wig.py

  • bam_stat.py

  • bed_bigwig_profile.py

  • bed_build_windows.py

  • bed_complement.py

  • bed_count_by_interval.py

  • bed_count_overlapping.py

  • bed_coverage.py

  • bed_coverage_by_interval.py

  • bed_diff_basewise_summary.py

  • bed_extend_to.py

  • bed_intersect.py

  • bed_intersect_basewise.py

  • bed_merge_overlapping.py

  • bed_rand_intersect.py

  • bed_subtract_basewise.py

  • bnMapper.py

  • clipping_profile.py

  • deletion_profile.py

  • div_snp_table_chr.py

  • divide_bam.py

  • find_in_sorted_file.py

  • geneBody_coverage.py

  • geneBody_coverage2.py

  • gene_fourfold_sites.py

  • get_scores_in_intervals.py

  • infer_experiment.py

  • inner_distance.py

  • insertion_profile.py

  • int_seqs_to_char_strings.py

  • interval_count_intersections.py

  • interval_join.py

  • junction_annotation.py

  • junction_saturation.py

  • lav_to_axt.py

  • lav_to_maf.py

  • line_select.py

  • lzop_build_offset_table.py

  • mMK_bitset.py

  • maf_build_index.py

  • maf_chop.py

  • maf_chunk.py

  • maf_col_counts.py

  • maf_col_counts_all.py

  • maf_count.py

  • maf_covered_ranges.py

  • maf_covered_regions.py

  • maf_div_sites.py

  • maf_drop_overlapping.py

  • maf_extract_chrom_ranges.py

  • maf_extract_ranges.py

  • maf_extract_ranges_indexed.py

  • maf_filter.py

  • maf_filter_max_wc.py

  • maf_gap_frequency.py

  • maf_gc_content.py

  • maf_interval_alignibility.py

  • maf_limit_to_species.py

  • maf_mapping_word_frequency.py

  • maf_mask_cpg.py

  • maf_mean_length_ungapped_piece.py

  • maf_percent_columns_matching.py

  • maf_percent_identity.py

  • maf_print_chroms.py

  • maf_print_scores.py

  • maf_randomize.py

  • maf_region_coverage_by_src.py

  • maf_select.py

  • maf_shuffle_columns.py

  • maf_species_in_all_files.py

  • maf_split_by_src.py

  • maf_thread_for_species.py

  • maf_tile.py

  • maf_tile_2.py

  • maf_tile_2bit.py

  • maf_to_axt.py

  • maf_to_concat_fasta.py

  • maf_to_fasta.py

  • maf_to_int_seqs.py

  • maf_translate_chars.py

  • maf_truncate.py

  • maf_word_frequency.py

  • mask_quality.py

  • mismatch_profile.py

  • nib_chrom_intervals_to_fasta.py

  • nib_intervals_to_fasta.py

  • nib_length.py

  • normalize_bigwig.py

  • one_field_per_line.py

  • out_to_chain.py

  • overlay_bigwig.py

  • prefix_lines.py

  • pretty_table.py

  • qv_to_bqv.py

  • random_lines.py

  • read_GC.py

  • read_NVC.py

  • read_distribution.py

  • read_duplication.py

  • read_hexamer.py

  • read_quality.py

  • split_bam.py

  • split_paired_bam.py

  • table_add_column.py

  • table_filter.py

  • tfloc_summary.py

  • tin.py

  • ucsc_gene_table_to_intervals.py

  • wiggle_to_array_tree.py

  • wiggle_to_binned_array.py

  • wiggle_to_chr_binned_array.py

  • wiggle_to_simple.py

Module

You can load the modules by:

module load biocontainers
module load rseqc

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 rseqc 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=rseqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers rseqc

# Your rseqc 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=rseqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers rseqc

# Your rseqc 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=rseqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers rseqc

# Your rseqc 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=rseqc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers rseqc

# Your rseqc workflow...

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

module --force purge
module biocontainers rseqc

# Your rseqc workflow...