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Salmon quant (version 1.10.1+galaxy2)

Select salmon quantification mode::

Select a reference transcriptome from your history or use a built-in index?:

Built-ins were indexed using default options

Salmon indices

Salmon index 0

Data inputs

Data input 0

Type of index:

When using quasi, orphaned reads will be considered when performing lightweight-alignment.

Discard orphan quasi:

Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist.

Validate mappings:

Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.

Consensus Slack:

The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise.

Allow Dovetail:

Allow dovetail mappings

Recover Orphans:

Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity.

Write Mappings to BAM File:

If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead

Consistent Hits:

Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart).

Quasi Coverage:

[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used.

File containing a mapping of transcripts to genes:

If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab.

Perform sequence-specific bias correction:

Perform fragment GC bias correction:

incompatPrior:

Sets the prior probability that an alignment that disagrees with the specified library type (orientation and strandedness) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do

Meta:

If you're using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.

Additional Options

Additional Options 0

Salmon is a lightweight method for quantifying transcript abundance from RNA–seq reads, combining a dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.

The salmon package contains 4 tools:

Index: creates a salmon index

Quant: quantifies a sample (Reads or mapping-based)

Alevin: Single-cell analysis

Quantmerge: Merges multiple quantifications into a single file

Galaxy divides these four into three separate tools in the IUC toolshed:

Salmon quant

Salmon quantmerge

Alevin