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
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