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