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.
Docker hub: https://hub.docker.com/r/pasapipeline/pasapipeline
Home page: https://github.com/PASApipeline/PASApipeline
- 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
You can load the modules by:
module load biocontainers
module load pasapipelineExample 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 -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
ml biocontainers pasapipeline