L |
Length of the biological read. For instance, 10xv1: 98 nt,
10xv2: 98 nt, 10xv3: 91 nt, Drop-seq: 50 nt. If in doubt check read length
in a fastq file for biological reads with the bash commands:
If the fastq file is gzipped, then do zcat your_file.fastq.gz | head on
Linux. If on Mac, then zcat < your_file.fastq.gz | head . Then you will see
lines with nucleotide bases. Copy one of those lines and determine its length
with str_length in R or echo -n <the sequence> | wc -c in
bash . Which file corresponds to biological reads depends on the particular
technology.
|
Genome |
Either a BSgenome or a XStringSet
object of genomic sequences, where the intronic sequences will be extracted
from. Use genomeStyles to check which styles are supported for
your organism of interest; supported styles can be interconverted. If the
style in your genome or annotation is not supported, then the style of
chromosome names in the genome and annotation should be manually set to be
consistent.
|
Transcriptome |
A XStringSet , a path to a fasta
file (can be gzipped) of the transcriptome which contains sequences of
spliced transcripts, or NULL . The transcriptome here will be concatenated
with the intronic sequences to give one fasta file. When NULL , the
transriptome sequences will be extracted from the genome
given the gene annotation, so it will be guaranteed that transcript IDs in
the transcriptome and in the annotation match. Otherwise, the type of
transcript ID in the transcriptome must match that in the gene annotation
supplied via argument X .
|
out_path |
Directory to save the outputs written to disk. If this
directory does not exist, then it will be created. Defaults to the current
working directory.
|
compress_fa |
Logical, whether to compress the output fasta file. If
TRUE , then the fasta file will be gzipped.
|
width |
Maximum number of letters per line of sequence in the output
fasta file. Must be an integer.
|
exon_option |
Character, indicating how exonic sequences should be
included in the kallisto index. Must be one of the following:
- full
The full cDNA sequences, which include the full exonic sequences,
will be used. This is the default.
- junction
Only the exon-exon junctions, with L-1 bases on each side
of the junctions, will be used.
|
Will throw error if validation fails. Returns a named list whose
first element is the normalized path to output directory, and whose second
element is the normalized path to the transcriptome file if specified.