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Input Parameters
bj8th edited this page Jul 22, 2021
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| Parameter | Description |
|---|---|
| sample_ccs | PacBio CCS reads (not required if SQANTI input provided) |
| gencode_gtf | GENCODE Comprehensive gene annotation. Link |
| gencode_transcript_fasta | GENCODE Protein-coding transcript sequences Link |
| gencode_translation_fasta | GENCODE Protein-coding transcript translation sequences |
| genome_fasta | Genome sequence, primary assembly (GRCh38) Link |
| fastq_read_1 (optional) | RNA-Seq fastq files. Used in STAR alignment to obtain junctions for the sample. |
| fastq_read_2 (optional) | RNA-Seq fastq files. Used in STAR alignment to obtain junctions for the sample. |
| star_genome_dir (optional) | STAR genome index (index is generated if fastq files provided and star_genome_dir not provided) |
| primers_fasta | Primers fasta file. used in IsoSeq (not required if SQANTI input provided) (example) |
| hexamer | Hexamer model provided by CPAT here |
| logit_model | Logit model provided by CPAT here |
| sqanti_classification (optional*) | SQANTI classification file |
| sqanti_fasta (optional*) | SQANTI corrected fasta file |
| sqanti_gtf (optional*) | SQANTI corrected gtf file |
| sample_kallisto_tpm | Sample Kallisto file |
| normalized_ribo_kallisto | Normalized Kallisto file |
| uniprot_protein_fasta | Uniprot Protein Isoforms fasta file Link |
| mass_spec (optional**) | Directory containing mass spec data. Data can be *.raw or *.mzml format |
| metamorpheus_toml (optional**) | Metamorpheus .toml file to use in mass spec. Not required to run proteomic analysis |
| rescue_resolve_toml (optional**) | Rescue and Resolve Metamorpheus .toml file. Required to run proteomic analysis |
*The pipeline does not run IsoSeq or SQANTI if all sqanti files are provided.
** If mass spec data is not provided then proteomic analysis is not done.
| Parameter | Description | Default Value |
|---|---|---|
| name | Name of pipeline run | false |
| outdir | Output directory of results to be stored | ./results |
| max_cpus | Number of CPUs a process can use | 8 |
| coding_score_cutoff | CPAT coding score cutoff. Remove ORFs with coding score below cutoff | 0.0 |
| min_junctions_after_stop_codon | Minimum number of junctions an ORF can have after stop codon to not be filtered. Only applies if protein classification is not pFSM or pNIC | 2 |
| lower_cpm | Lower CPM for filtering of high confidence space | 3 |
| lower_kb | Lower gene nucleotide length for filtering of high confidence space | 1 |
| upper_kb | Upper gene nucleotide length for filtering of high confidence space | 4 |
Sheynkman-Lab