Pasapipeline

Introduction

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced ‘pass-uh’), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

For more information, please check:
Docker hub: https://hub.docker.com/r/pasapipeline/pasapipeline
Home page: https://github.com/PASApipeline/PASApipeline

Note

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

Versions

Cluster

Version(s)

ANVIL

2.5.2-devb

BELL

2.5.2-devb

GAUTSCHI

2.5.2-devb

NEGISHI

2.5.2-devb

SCHOLAR

2.5.2-devb

Commands

  • pasa

  • Launch_PASA_pipeline.pl

  • GMAP_multifasta_processor.pl

  • blat_to_btab.pl

  • blat_to_cdna_clusters.pl

  • blat_top_hit_extractor.pl

  • ensure_single_valid_alignment_per_cdna_per_cluster.pl

  • errors_to_newalign_btabs.pl

  • extract_FL_transdecoder_entries.pl

  • get_failed_transcripts.pl

  • gmap_to_btab.pl

  • import_GMAP_gff3.pl

  • pasa_alignment_assembler_textprocessor.pl

  • pasa_asmbls_to_training_set.extract_reference_orfs.pl

  • polyCistronAnalyzer.pl

  • process_BLAT_alignments.pl

  • process_GMAP_alignments_gff3_chimeras_ok.pl

  • process_PBLAT_alignments.pl

  • process_minimap2_alignments.pl

  • pslx_to_gff3.pl

  • run_spliced_aligners.pl

  • sim4_to_btab.pl

  • Annotation_store_preloader.dbi

  • Load_Current_Gene_Annotations.dbi

  • PASA_transcripts_and_assemblies_to_GFF3.dbi

  • UTR_category_analysis.dbi

  • __drop_many_mysql_dbs.dbi

  • alignment_assembly_to_gene_models.dbi

  • alt_splice_AAT_alignment_generator.dbi

  • assemble_clusters.dbi

  • assembly_db_loader.dbi

  • assign_clusters_by_gene_intergene_overlap.dbi

  • assign_clusters_by_stringent_alignment_overlap.dbi

  • build_comprehensive_transcriptome.dbi

  • build_comprehensive_transcriptome.tabix.dbi

  • cDNA_annotation_comparer.dbi

  • cDNA_annotation_updater.dbi

  • classify_alt_splice_as_UTR_or_protein.dbi

  • classify_alt_splice_isoforms.dbi

  • classify_alt_splice_isoforms_per_subcluster.dbi

  • comprehensive_alt_splice_report.dbi

  • compute_gene_coverage_by_incorporated_PASA_assemblies.dbi

  • create_mysql_cdnaassembly_db.dbi

  • create_sqlite_cdnaassembly_db.dbi

  • describe_alignment_assemblies.dbi

  • describe_alignment_assemblies_cgi_convert.dbi

  • drop_mysql_db_if_exists.dbi

  • dump_annot_store.dbi

  • dump_valid_annot_updates.dbi

  • extract_regions_for_probe_design.dbi

  • extract_skipped_exons.dbi

  • extract_transcript_alignment_clusters.dbi

  • find_FL_equivalent_support.dbi

  • find_alternate_internal_exons.dbi

  • get_antisense_transcripts.dbi

  • import_custom_alignments.dbi

  • import_spliced_alignments.dbi

  • invalidate_RNA-Seq_assembly_artifacts.dbi

  • invalidate_single_exon_ESTs.dbi

  • mapPolyAsites_to_genes.dbi

  • pasa_asmbl_genes_to_GFF3.dbi

  • pasa_asmbls_to_training_set.dbi

  • polyA_site_summarizer.dbi

  • polyA_site_transcript_mapper.dbi

  • populate_alignments_via_btab.dbi

  • populate_ath1_cdnas.dbi

  • populate_cdna_clusters.dbi

  • populate_mysql_assembly_alignment_field.dbi

  • populate_mysql_assembly_sequence_field.dbi

  • purge_PASA_database.dbi

  • purge_annot_comparisons.dbi

  • reassign_clusters_via_valid_align_coords.dbi

  • reconstruct_FL_isoforms_from_parts.dbi

  • report_alt_splicing_findings.dbi

  • reset_to_prior_to_assembly_build.dbi

  • retrieve_assembly_sequences.dbi

  • set_spliced_orient_transcribed_orient.dbi

  • splicing_events_in_subcluster_context.dbi

  • splicing_variation_to_splicing_event.dbi

  • subcluster_builder.dbi

  • subcluster_loader.dbi

  • test_assemble_clusters.dbi

  • test_mysql_connection.dbi

  • update_alignment_status.dbi

  • update_clusters_coordinates.dbi

  • update_fli_status.dbi

  • update_spliced_orient.dbi

  • upload_cdna_headers.dbi

  • upload_transcript_data.dbi

  • validate_alignments_in_db.dbi

Module

You can load the modules by:

module load biocontainers
module load pasapipeline

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

module --force purge
module biocontainers pasapipeline

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

module --force purge
module biocontainers pasapipeline

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

module --force purge
module biocontainers pasapipeline

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

module --force purge
module biocontainers pasapipeline

# Your pasapipeline workflow...

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

module --force purge
module biocontainers pasapipeline

# Your pasapipeline workflow...