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SRAAlignment_BRC4.md

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SRAAlignment_BRC4

Module Bio::EnsEMBL::EGPipeline::PipeConfig::SRAAlignment_BRC4_conf

Perform RNA(DNA) short read aligments

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::SRAAlignment_BRC4_conf \
    $($CMD details hive) \
    --hive_force_init 1 \
    --reg_conf $REG_FILE \
    --pipeline_dir temp/rnaseq \
    --datasets_file $DATASETS \
    --results_dir $OUTPUT \
    ${OTHER_OPTIONS}

Parameters

option default value meaning
--pipeline_name sra_alignment_brc4_{ensembl_release} name of the hive pipeline
--results_dir directory where the final alignments are stored
--pipeline_dir temp directory
--index_dir {pipeline_dir}/index temp directory where the genomes files are extracted
--datasets_file List of datasets following the schema in brc4_rnaseq_schema.json
--dna_seq 0 Run the pipeline for DNA-Seq instead of RNA-Seq short reads
--global_bw 0 A global BigWig file will be created alongside the analysis
--skip_cleanup 0, or 1 if using --dna_seq Do not remove intermediate files from the results dir (that includes the bam files)
--fallback_ncbi 0 If download from ENA fails, try to download from SRA
--force_ncbi 0 Force download data from SRA instead of ENA
--sra_dir Where to find fastq-dump (in case it is not in your path)
-redo_htseqcount 0 Special pipeline path, where no alignment is done, but a previous alignment is reused to recount features coverage (--alignments_dir becomes necessary)
--alignments_dir Where to find previous alignments. Needed for --redo_htseqcount 1
-infer_metadata 1 Automatically infer the reads metadata: single/paired-end, stranded/unstranded, and in which direction. Otherwise, use the values from the datasets_file

Rare parameters

option default value meaning
-trim_reads 0 Trim reads before doing any alignment
-trimmomatic_bin Trimmomatic path if using --trim_reads
-trim_adapters_pe Paired-end adapter path if using --trim_reads
-trim_adapters_se Single-end adapter path if using --trim_reads
--threads 4 Number of threads to use for various programs
--samtobam_memory 16,000 Memory to use for the conversion/sorting SAM -> BAM (in MB)
--repeat_masking soft What masking to use when extracting the genomes sequences
--max_intron 1 Wether to compute the max intron from the current gene models

Notes

Parts

A few generic from Common::RunnableDB.

A few from EnsEMBL::ENA::SRA.

A few from BRC4Aligner.