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 its website: https://biocontainers.pro/tools/rseqc and its home page: http://rseqc.sourceforge.net.

Versions

  • 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 -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
ml biocontainers rseqc

bam_stat.py -i *.bam -q 30