Command Line Options:¶

-v [ --version ]

print version string

-h [ --help ]

produce help message

-t [ --transcripts ] arg

Transcript fasta file.

-k [ --kmerLen ] arg (=31) The size of k-mers that should be used for the

quasi index.

-i [ --index ] arg

salmon index.

--gencode

This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first '|' character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.

--keepDuplicates

This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts. If this flag is passed, then duplicate transcripts that appear in the input will be retained and quantified separately.

-p [ --threads ] arg (=2)

Number of threads to use (only used for computing bias features)

--perfectHash

[quasi index only] Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct

--type arg (=quasi)

The type of index to build; the only option is "quasi" in this version of salmon.