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.
- --features
- This flag will expect the input reference to be in the tsv file format,
and will split the feature name at the first 'tab' character. These
reduced names will be used in the output and when looking for the sequence
of the features.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 during indexing.
- --keepFixedFasta
- Retain the fixed fasta file (without short transcripts and duplicates,
clipped, etc.) generated during indexing
- -f [ --filterSize ]
arg (=-1) The size of the Bloom filter that will be used
- by TwoPaCo during indexing. The filter will be of size 2^{filterSize}. The
default value of -1 means that the filter size will be
automatically set based on the number of distinct k-mers in the input, as
estimated by nthll.
- --tmpdir
arg
- The directory location that will be used for TwoPaCo temporary files; it
will be created if need be and be removed prior to indexing completion.
The default value will cause a (temporary) subdirectory of the salmon
index directory to be used for this purpose.
- --sparse
- Build the index using a sparse sampling of k-mer positions This will
require less memory (especially during quantification), but will take
longer to construct and can slow down mapping / alignment
- -d [ --decoys ]
arg
- Treat these sequences ids from the reference as the decoys that may have
sequence homologous to some known transcript. for example in case of the
genome, provide a list of chromosome name --- one per line
- --type arg
(=puff)
- The type of index to build; the only option is "puff" in this
version of salmon.