salmon_index - highly-accurate, transcript-level quantification
estimates from RNA-seq data
Index ========== Creates a salmon index.
- -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.