docs/ARGUMENTS.md

In lehner-lab/DiMSum: A pipeline for processing deep mutational scanning data

< Table Of Contents

Command-line Arguments

• General
• TRIM Arguments
• ALIGN Arguments
• PROCESS Arguments
• ANALYSE Arguments
• FASTQ Files
• Multiplexed FASTQ Files
• Custom Variant Count File
• Barcoded Library Design
• Trans Library Design

General

• --runDemo Run the DiMSum Demo (default:F)
• --projectName Project name and directory where results are to be saved (default:'DiMSum_Project')
• --experimentDesignPath Path to Experimental Design File (required if '--runDemo'=F)
• --outputPath Path to directory to use for output files (default:'./' i.e. current working directory)
• --retainIntermediateFiles Should intermediate files be retained? Intermediate files can be many gigabytes, but are required to rerun DiMSum starting at intermediate pipeline stages (default:F)
• --startStage (Re-)Start DiMSum at a specific pipeline stage (default:0)
• --stopStage Stop DiMSum at a specific pipeline stage (default:5)
• --numCores Number of available CPU cores. All pipeline stages make use of parallel computing to decrease runtime if multiple cores are available (default:1)

TRIM Arguments

• --cutadapt5First Sequence of 5' constant region to be trimmed from first (or only) read (optional). Alternatively, both 5' and 3' optional/required constant region sequences can be specified with this argument e.g. '--cutadapt5First'='ACGT;optional...GGCC;required'.
• --cutadapt5Second Sequence of 5' constant region to be trimmed from second read in pair (optional). Alternatively, both 5' and 3' optional/required constant region sequences can be specified with this argument '--cutadapt5Second'='ACGT;optional...GGCC;required'.
• --cutadapt3First Sequence of 3' constant region to be trimmed from first (or only) read (default: reverse complement of '--cutadapt5Second')
• --cutadapt3Second Sequence of 3' constant region to be trimmed from second read in pair (default: reverse complement of '--cutadapt5First')
• --cutadaptMinLength Discard reads shorter than LENGTH after trimming (default:50)
• --cutadaptErrorRate Maximum allowed error rate for trimming constant regions (default:0.2)
• --cutadaptOverlap Minimum overlap between read and constant region for trimming (default:3)
• --cutadaptCut5First Remove fixed number of bases from start (5') of first (or only) read before constant region trimming (optional)
• --cutadaptCut5Second Remove fixed number of bases from start (5') of second read in pair before constant region trimming (optional)
• --cutadaptCut3First Remove fixed number of bases from end (3') of first (or only) read before constant region trimming (optional)
• --cutadaptCut3Second Remove fixed number of bases from end (3') of second read in pair before constant region trimming (optional)

ALIGN Arguments

• --vsearchMinQual Minimum Phred base quality score required to retain read or read pair (default:30)
• --vsearchMaxee Maximum number of expected errors tolerated to retain read or read pair (default:0.5)
• --vsearchMinovlen Discard read pair if the alignment length is shorter than this (default:10)

PROCESS Arguments

• --reverseComplement Reverse complement sequences before variant processing? (default:F)
• --wildtypeSequence Wild-type nucleotide sequence (A/C/G/T). Lower-case bases (a/c/g/t) indicate internal constant regions to be removed (required if '--runDemo'=F)
• --permittedSequences Nucleotide sequence of IUPAC ambiguity codes (A/C/G/T/R/Y/S/W/K/M/B/D/H/V/N) with length matching the number of mutated positions (i.e upper-case letters) in '--wildtypeSequence' (default:N i.e. any substitution mutation allowed)
• --sequenceType Coding potential of sequence: either 'noncoding', 'coding' or 'auto'. If the specified wild-type nucleotide sequence ('--wildtypeSequence') has a valid translation without a premature STOP codon, it is assumed to be 'coding' (default:'auto')
• --mutagenesisType Whether mutagenesis was performed at the nucleotide or codon/amino acid level; either 'random' or 'codon' (default:'random')
• --indels Indel variants to be retained: either 'all', 'none' or a comma-separated list of sequence lengths (default:'none')
• --maxSubstitutions Maximum number of nucleotide or amino acid substitutions for coding or non-coding sequences respectively (default:2)
• --mixedSubstitutions For coding sequences, are nonsynonymous variants with silent/synonymous substitutions in other codons allowed? (default:F)

ANALYSE Arguments

• --fitnessMinInputCountAll Minimum input read count (in all replicates) to be retained during fitness calculations (default:0). Alternatively, thresholds can be applied to variants with specific numbers of nucleotide substitutions as follows 'edit_distance:threshold' e.g. '--fitnessMinInputCountAll'='1:100,2:10,3:10' (unspecified variants are discarded).
• --fitnessMinInputCountAny Minimum input read count (in any replicate) to be retained during fitness calculations (default:0). Alternatively, thresholds can be applied to variants with specific numbers of nucleotide substitutions as follows 'edit_distance:threshold' e.g. '--fitnessMinInputCountAny'='1:100,2:10,3:10' (unspecified variants are discarded).
• --fitnessMinOutputCountAll Minimum output read count (in all replicates) to be retained during fitness calculations (default:0). Alternatively, thresholds can be applied to variants with specific numbers of nucleotide substitutions as follows: 'edit_distance:threshold' e.g. '--fitnessMinOutputCountAll'='1:100,2:10,3:10' (unspecified variants are discarded).
• --fitnessMinOutputCountAny Minimum output read count (in any replicates) to be retained during fitness calculations (default:0). Alternatively, thresholds can be applied to variants with specific numbers of nucleotide substitutions as follows: 'edit_distance:threshold' e.g. '--fitnessMinOutputCountAny'='1:100,2:10,3:10' (unspecified variants are discarded).
• --fitnessNormalise Normalise fitness values to minimise inter-replicate differences (default:T)
• --fitnessErrorModel Fit fitness error model (default:T)
• --retainedReplicates Comma-separated list of (integer) experiment replicates to retain or 'all' (default:'all')

FASTQ files

• --fastqFileDir Path to directory containing input FASTQ files (required for WRAP)
• --fastqFileExtension FASTQ file extension (default:'.fastq')
• --gzipped Are FASTQ files gzipped? (default:T)
• --stranded Is the library design stranded? (default:T)
• --paired Is the library design paired-end? (default:T)
• --experimentDesignPairDuplicates Are multiple instances of FASTQ files in the Experimental Design File permitted? (default:F)

Multiplexed FASTQ Files

• --barcodeDesignPath Path to Barcode Design File (tab-separated plain text file with barcode design)
• --barcodeErrorRate Maximum allowed error rate for barcode to be matched (default:0.25)

Custom Variant Count File

• --countPath Path to Variant Count File for analysis with STEAM only (tab-separated plain text file with sample counts for all variants)

Barcoded Library Design

• --barcodeIdentityPath Path to Variant Identity File (tab-separated plain text file mapping barcodes to variants)

Alternative Reference Sequences

• --synonymSequencePath Path to Synonym Sequences File (plain text file with one coding nucleotide sequence per line)

Trans Library Design

• --transLibrary Paired-end reads correspond to distinct molecules? (default:F)
• --transLibraryReverseComplement Reverse complement second read in pair (default:F)

lehner-lab/DiMSum documentation built on April 10, 2024, 4:15 a.m.