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.
Versions
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 -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