Make and load linked transcriptomes (linked GTF and FASTA)

makeLinkedTxome() reads the digest associated with a salmon index at indexDir, and persistently links it to metadata (alternatively the digest string itself and an indexName can be provided). Linked metadata includes key information about the transcriptome, including the source, organism, release, and genome (these are custom character strings), as well as the locations (e.g. local, HTTP, or FTP) for one or more fasta files and one gtf file. loadLinkedTxome() loads this information from a JSON file. See Details.

Usage

makeLinkedTxome(
  digest = NULL,
  indexName,
  indexDir = NULL,
  source,
  organism,
  release,
  genome,
  fasta,
  gtf,
  write = TRUE,
  jsonFile
)

loadLinkedTxome(jsonFile)

Arguments

digest: the full digest as character string, (this or indexDir is required, only one should be specified)
indexName: a name for the index when storing the linkedTxome, required if providing the digest string, suggest using the basename of the FASTA file and the software used, e.g. "gencode.vXX_salmon-0.XX.Y"
indexDir: the local path to the salmon index (this or digest is required, only one should be specified)
source: the source of transcriptome (e.g. "de-novo"). Note: if you specify "GENCODE" or "Ensembl", this will trigger behavior by tximeta that may not be desired: e.g. attempts to download canonical transcriptome data from AnnotationHub (unless useHub=FALSE when running tximeta) and parsing of Ensembl GTF using ensembldb (which may fail if the GTF file has been modified). For transcriptomes that are defined by local GTF files, it is recommended to use the terms "LocalGENCODE" or "LocalEnsembl". Setting "LocalEnsembl" will also strip version numbers from the FASTA transcript IDs to enable matching with the Ensembl GTF.
organism: organism (e.g. "Homo sapiens")
release: release number (e.g. "27")
genome: genome (e.g. "GRCh38", or "none")
fasta: location(s) for the FASTA transcript sequences (of which the transcripts used to build the index is equal or a subset). This can be a local path, or an HTTP or FTP URL
gtf: location for the GTF/GFF file (of which the transcripts used to build the index is equal or a subset). This can be a local path, or an HTTP or FTP URL While the fasta argument can take a vector of length greater than one (more than one FASTA file containing transcripts used in indexing), the gtf argument has to be a single GTF/GFF file. This can also be a serialized GRanges object (location of a .rds file) imported with rtracklayer. If transcripts were added to a standard set of reference transcripts (e.g. fusion genes, or pathogen transcripts), it is recommended that the tximeta user would manually add these to the GTF/GFF file, and post the modified GTF/GFF publicly, such as on Zenodo. This enables consistent annotation and downstream annotation tasks, such as by summarizeToGene().
write: logical, should a JSON file be written out which documents the transcriptome digest and metadata? (default is TRUE)
jsonFile: the path to the json file for the linkedTxome

Value

nothing, the function is run for its side effects

Details

makeLinkedTxome() links the information about the transcriptome used for quantification in two ways:

the function will store a record in tximeta's cache such that future import of quantification data will automatically access and parse the GTF as if the transcriptome were one of those automatically detected by tximeta. Then all features of tximeta (e.g. summarization to gene, programmatic adding of IDs or metadata) will be available;
it will by default write out a JSON file that can be shared, or posted online, and which can be read by loadLinkedTxome() which will store the information in tximeta's cache. This should make the full quantification-import pipeline computationally reproducible / auditable even for transcriptomes which differ from those provided by references (GENCODE, Ensembl, RefSeq).

For further details please see the "Linked transcriptomes" section of the tximeta vignette.

This function can be used in combination with inspectDigests() and oarfish data from importData(), when multiple reference transcript sets have been indexed. See also makeLinkedTxpData().

Examples


# point to a salmon quantification file with an additional artificial transcript
dir <- system.file("extdata/salmon_dm", package="tximportData")
file <- file.path(dir, "SRR1197474.plus", "quant.sf")
coldata <- data.frame(files=file, names="SRR1197474", sample="1",
                      stringsAsFactors=FALSE)

# now point to the salmon index itself to create a linkedTxome
# as the index will not match a known txome
indexDir <- file.path(dir, "Dm.BDGP6.22.98.plus_salmon-0.14.1")

# point to the source FASTA and GTF:
baseFTP <- "ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/"
fastaFTP <- c(
  paste0(baseFTP,
    c("cdna/Drosophila_melanogaster.BDGP6.22.cdna.all.fa.gz",
      "ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz")),
  "extra_transcript.fa.gz"
)
gtfPath <- file.path(dir, "Drosophila_melanogaster.BDGP6.22.98.plus.gtf.gz")

# now create a linkedTxome, linking the salmon index to its FASTA and GTF sources
makeLinkedTxome(indexDir=indexDir, source="LocalEnsembl", organism="Drosophila melanogaster",
                release="98", genome="BDGP6.22", fasta=fastaFTP, gtf=gtfPath, write=FALSE)
#> reading digest from indexDir: .../Dm.BDGP6.22.98.plus_salmon-0.14.1
#> saving linkedTxome in bfc

# to clear the entire linkedTxome table
# (don't run unless you want to clear this table!)
# bfcloc <- getTximetaBFC()
# bfc <- BiocFileCache(bfcloc)
# bfcremove(bfc, bfcquery(bfc, "linkedTxomeTbl")$rid)