salmon quant

Reference Code backup Executable files

Perform dual-phase, selective-alignment-based estimation of transcript abundance from RNA-seq reads

Category

Gene Expression Analysis

Usage

salmon quant [options] -t transcripts.fa -l <LIBTYPE> -a aln.bam -o salmon_quant

Manual

Required arguments

  • -l, --libType string: Format string describing the library type
  • -i, --index string: Salmon index
  • -r, --unmatedReads string: List of files containing unmated reads (e.g., single-end reads)
  • -1, --mates1 string: File containing the #1 mates
  • -2, --mates2 string: File containing the #2 mates

Options

Basic options
  • -v, --version: Print version string
  • -h, --help: Produce help message
  • -o, --output string: Output quantification directory
  • --seqBias: Perform sequence-specific bias correction
  • --gcBias [beta for single-end reads]: Perform fragment GC bias correction
  • --posBias: Perform positional bias correction
  • -p, --threads int (=88): The number of threads to use concurrently
  • --incompatPrior float (=0): Set the prior probability for incompatible alignments based on library type
  • -g, --geneMap string: File containing a mapping of transcripts to genes
  • --auxTargetFile string: A file containing a list of "auxiliary" targets
  • --meta: Disable parts of the abundance estimation model for metagenomic data
Options specific to mapping mode
  • --discardOrphansQuasi [selective-alignment mode only]: Discard orphan mappings in selective-alignment mode
  • --validateMappings [*deprecated*]: No effect (selective-alignment is the default)
  • --consensusSlack float (=0.35) [selective-alignment mode only]: The amount of slack allowed in the selective-alignment filtering mechanism
  • --preMergeChainSubThresh float (=0.75) [selective-alignment mode only]: The threshold of sub-optimal chains that will be retained
  • --postMergeChainSubThresh float (=0.9) [selective-alignment mode only]: The threshold of sub-optimal chain pairs that will be retained after merging
  • --orphanChainSubThresh float (=0.95) [selective-alignment mode only]: Global sub-optimality threshold for chains corresponding to orphan mappings
  • --scoreExp int (=1) [selective-alignment mode only]: Factor by which sub-optimal alignment scores are downweighted
  • --minScoreFraction float [selective-alignment mode only]: Fraction of the optimal alignment score required for a valid alignment
  • --mismatchSeedSkip int (=3) [selective-alignment mode only]: Skip length for mismatched seeds during extension
  • --disableChainingHeuristic [selective-alignment mode only]: Disable chaining heuristic for seed chaining
  • --decoyThreshold float (=1) [selective-alignment mode only]: Threshold for alignment score compared to decoy alignments
  • --ma int (=2) [selective-alignment mode only]: Match score
  • --mp int (=-4) [selective-alignment mode only]: Mismatch penalty
  • --go int (=6) [selective-alignment mode only]: Gap opening penalty
  • --ge int (=2) [selective-alignment mode only]: Gap extension penalty
  • --bandwidth int (=15) [selective-alignment mode only]: Bandwidth for ksw2 alignment
  • --allowDovetail [selective-alignment mode only]: Allow dovetailing mappings
  • --recoverOrphans [selective-alignment mode only]: Attempt to recover the mates of orphaned reads
  • --mimicBT2 [selective-alignment mode only]: Mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags
  • --mimicStrictBT2 [selective-alignment mode only]: Mimic strict parameters used by RSEM+Bowtie2
  • --softclip [selective-alignment mode only (experimental)]: Allow soft-clipping of reads during selective-alignment
  • --softclipOverhangs [selective-alignment mode only]: Allow soft-clipping of overhanging reads
  • --fullLengthAlignment [selective-alignment mode only]: Perform selective alignment over the full length of the read
  • --hardFilter [selective-alignment mode only]: Discard mappings with sub-optimal alignment score
  • --minAlnProb float (=1e-05) [selective-alignment mode only]: Minimum alignment probability for valid mappings
  • -z, --writeMappings [=arg(=-)]: Write selective-alignment results in SAM-compatible format
  • --writeQualities: Include quality strings in the output SAM file (increases file size)
  • --hitFilterPolicy string (=AFTER) [selective-alignment mode only]: Policy for filtering hits in selective alignment (BEFORE, AFTER, BOTH, NONE)
Advanced options
  • --alternativeInitMode [Experimental]: Use an alternative strategy to initialize the EM / VBEM algorithm
  • --auxDir string (=aux_info): Sub-directory where auxiliary information will be written
  • --skipQuant: Skip performing transcript quantification
  • --dumpEq: Dump simple equivalence class counts computed during mapping or alignment
  • -d, --dumpEqWeights float (=0.65): Dump conditional probabilities associated with transcripts
  • --minAssignedFrags int (=10): Minimum number of fragments required for quantification
  • --reduceGCMemory: Use a memory-efficient representation for fragment GC content
  • --biasSpeedSamp int (=5): Value for down-sampling fragment length PMF for bias correction
  • --fldMax int (=1000): Maximum fragment length to consider
  • --fldMean int (=250): Mean used in the fragment length distribution prior
  • --fldSD int (=25): Standard deviation used in the fragment length distribution prior
  • -f, --forgettingFactor float (=0.65): Forgetting factor used in online learning schedule
  • --initUniform: Initialize offline inference with uniform parameters
  • --maxOccsPerHit int (=1000): Maximum occurrences for hits to be considered
  • -w, --maxReadOcc int (=200): Reads mapping to more than this many places won't be considered
  • --maxRecoverReadOcc int (=2500): Try to recover mappings for reads with fewer than this many mappings
  • --noLengthCorrection [experimental]: Disable length correction for transcript abundance
  • --noEffectiveLengthCorrection: Disable effective length correction for fragment probability
  • --noSingleFragProb: Disable estimation of fragment length probability for single-end reads or orphans
  • --noFragLengthDist [experimental]: Don't consider concordance with the learned fragment length distribution
  • --noBiasLengthThreshold [experimental]: Disable threshold on how short bias correction can make effective lengths
  • --numBiasSamples int (=2000000): Number of fragment mappings for learning sequence-specific bias model
  • --numAuxModelSamples int (=5000000): Number of samples for training auxiliary model parameters
  • --numPreAuxModelSamples int (=5000): Number of initial samples without applying auxiliary models
  • --useEM: Use the traditional EM algorithm for optimization
  • --useVBOpt [default]: Use the Variational Bayesian EM
  • --rangeFactorizationBins int (=4): Factorize the likelihood for more fine-grained factorization
  • --numGibbsSamples int (=0): Number of Gibbs sampling rounds to perform
  • --noGammaDraw: Disable drawing transcript fractions from a Gamma distribution during Gibbs sampling
  • --numBootstraps int (=0): Number of bootstrap samples to generate (mutually exclusive with Gibbs sampling)
  • --bootstrapReproject: Learn parameter distribution from bootstrapped counts but reproject parameters onto original equivalence class counts
  • --thinningFactor int (=16): Number of steps to discard for every sample kept from the Gibbs chain
  • -q, --quiet: Be quiet while doing quantification (don't write informative output to the console)
  • --perTranscriptPrior: Interpret the prior as a transcript-level prior
  • --perNucleotidePrior: Interpret the prior as a nucleotide-level prior
  • --sigDigits int (=3): Number of significant digits to write in output
  • --vbPrior float (=0.01): Prior used in the VBEM algorithm
  • --writeOrphanLinks: Write transcripts linked by orphaned reads
  • --writeUnmappedNames: Write the names of unmapped reads to a file

 

File formats this tool works with
BAM

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