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RNAGenes.md

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RNAGenes

Module Bio::EnsEMBL::EGPipeline::PipeConfig::RNAGenes_conf

This pipeline annotates RNA genes based on Rfam alignments, tRNAscan predictions, and miRBase data. A subset of the alignments produced by the RNAFeatures_conf (doc), with strict taxonomic filtering, is used as a requisite.

Prerequisites

A registry file with the locations of the core database server(s) and the production database (or -production_db $PROD_DB_URL specified).

How to run

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::RNAGenes_conf \
    $($CMD details script) \
    -hive_force_init 1\
    -registry $REG_FILE \
    -production_db "$($PROD_SERVER details url)""$PROD_DBNAME" \
    -pipeline_tag "_${SPECIES_TAG}" \
    -pipeline_dir $OUT_DIR/rna_genes \
    -species $SPECIES \
    -eg_pipelines_dir $ENS_DIR/ensembl-production-imported \
    -all_new_species 1 \
    -run_context vb \
    ${OTHER_OPTIONS} \
    2> $OUT_DIR/init.stderr \
    1> $OUT_DIR/init.stdout

SYNC_CMD=$(cat $OUT_DIR/init.stdout | grep -- -sync'$' | perl -pe 's/^\s*//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -sync

LOOP_CMD=$(cat $OUT_DIR/init.stdout | grep -- -loop | perl -pe 's/^\s*//; s/\s*#.*$//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -reg_file $REG_FILE -loop

$SYNC_CMD 2> $OUT_DIR/sync.stderr 1> $OUT_DIR/sync.stdout
$LOOP_CMD 2> $OUT_DIR/loop.stderr 1> $OUT_DIR/loop.stdout

Parameters / Options

option default value meaning
-species species to process, several -species options are possible
-pipeline_dir directory to store results to
-registry registry file with the locations of the core DBs and production DB
-production_db connection URL for the production DB; provide if no production DB is in the registry
-old_registry registry file with the locations of the core DBs for the previous release; no need if annotating only new genomes
-all_new_species 0 Stop doing stable ID, all species are assumed to be new; 1 -- to disable mapping
-use_cmscan 1 create genes from cmscan (Rfam mostly) alignments; 0 -- to skip
-use_trnascan 1 create genes from tRNAscan alignments; 0 -- to skip
-use_mirbase 1 create genes from mirBase alignments; 0 -- to skip
-run_context eg style of the stable identifiers: eg -- ENSRNA\d{9} like; vb -- use species.stable_id_prefix from the core DB metatable
-gene_source species.division from meta if defined; Ensembl -- otherwise name to use as a gene source
-mirbase_source_logic_name mirbase logic_name of the source alignments (already existing in the DB)
-mirbase_target_logic_name mirbase_gene logic_name for the genes to be created
-trnascan_source_logic_name trnascan_align logic_name of the source alignments (already existing in the DB)
-trnascan_target_logic_name trnascan_gene logic_name for the genes to be created
-rfam_version RFAM_VERSION set rfam_version to be included into default -cmscan_source_logic_name and -cmscan_target_logic_name values
-cmscan_source_logic_name cmscan_rfam_${rfam_version}_lca logic_name of the source alignments (default _lca assumes strict taxonomic filtering was used)
-cmscan_target_logic_name rfam_${rfam_version}_gene logic_name for the genes to be created
-id_db_host ENSEMBL_ENA_IDENTIFIERS_HOST connection details for the stable IDs DB
-id_db_port ENSEMBL_ENA_IDENTIFIERS_PORT connection details for the stable IDs DB
-id_db_user ENSEMBL_ENA_IDENTIFIERS_USER connection details for the stable IDs DB
-id_db_dbname ENSEMBL_ENA_IDENTIFIERS_DBNAME connection details for the stable IDs DB
-id_db_pass connection details for the stable IDs DB
-pipeline_tag Tag to append to the default -pipeline_name
-pipeline_name rna_genes_${ENS_VERSION}_<pipeline_tag> The hive database name will be ${USER}_${pipeline_name}
-production_lookup 1 Fetch analysis display name, description and web data from the production database; 0 -- to disable

Notes

Filtering

The taxonomic filtering itself, if enabled, for the RNAFeatures_conf (doc), removes many false positives. This pipeline assumes that RNA gene creation is conservative, and expects the taxonomic filtering be based on shared ancestry (rather than at the level of divisions).

A few filters applied automatically:

  • regulatory elements (everything with "misc_RNA" biotype) are filtered out;
  • palindromic RNA sequences can lead to overalpping credible hits (on the same or different strand), only one such alignment is picked to be converted to a gene, based on the better E-value.

miRBase alignments are trusted and not filtered.

cmscan filters can be tweaked using these pipeline options (see Inferal docs for some details):

option default value meaning
-evalue_threshold 1e-6 cmscan E-value threshold
-truncated 0 allow processing of truncated alignments; 1 -- partial genes are allowed
-nonsignificant 0 allow processing of non-significant alignments; 1 -- to allow
-bias_threshold 0.3 maximum degree of allowable GC/AT bias
-has_structure 1 only use features if they have structure; 0 -- allow to use features lacking structure
-allow_repeat_overlap 1 allow genes which overlap a repeat feature; 0 -- to disallow (not recommended)
-allow_coding_overlap 0 allow genes which overlap a protein-coding exon; 1 -- to allow
-maximum_per_hit_name { pre_miRNA' => 100, } limits on usage/sharing of the same hit(model) name

tRNAscan filters:

  • always applied:
    • tRNA genes are not allowed to overlap repeat regions
    • tRNA genes are not allowed to overlap protein-coding exons

Configurable:

option default value meaning
-score_threshold 40 a threshold for the COVE score

Preserving stable IDs between re-runs / releases

There's an option to preserve stable IDs between releases and reruns runs using -id_db_* database options.

Parts

A few generic from Common::RunnableDB.

A few from RNAFeatures.