TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
trust4(
file1,
ref_coordinate,
...,
file2 = NULL,
mode = NULL,
ref_annot = NULL,
ofile = NULL,
odir = getwd(),
trust4 = NULL
)trust4_imgt_annot(
species = "Homo_sapien",
...,
ofile = "IMGT+C.fa",
odir = getwd(),
perl = NULL
)
trust4_gene_names(imgt_annot, ofile = "bcr_tcr_gene_name.txt", odir = getwd())
A command object.
Path to bam file or fastq file.
Path to the fasta file coordinate and sequence of V/D/J/C genes.
trust4: <dynamic dots> Additional arguments passed to run-trust4 command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(run-trust4()).
trust4_imgt_annot: <dynamic dots> Additional arguments passed to trust4_imgt_annot command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(trust4_imgt_annot()).
Path to the second paired-end read fastq file, only used for
mode = "fastq".
One of "bam" or "fastq". If NULL, will be inferred from
file1.
Path to detailed V/D/J/C gene reference file, such as from IMGT database. (default: not used). (recommended).
trust4: Prefix of output files. (default: inferred from file prefix).
trust4_imgt_annot: Output file name.
trust4_gene_names: Output file name.
A string of path to the output directory.
A string of path to run-trust4 command.
Species to extract IMGT annotation, details see https://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory/.
A string of path to perl command.
Path of IMGT annotation file, created via
trust4_imgt_annot.
cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_conda()
cmd_on_start()/cmd_on_exit()
cmd_on_succeed()/cmd_on_fail()
cmd_parallel()
Other commands:
allele_counter(),
cellranger(),
conda(),
fastq_pair(),
gistic2(),
kraken2(),
kraken_tools(),
perl(),
pyscenic(),
python(),
samtools(),
seqkit()