windows_pipeline_isoforms {FLAMES} | R Documentation

## Windows Pipeline - Find Isoforms

### Description

This is the second step in the 3 step Windows FLAMES pipeline. Following this step, read realignment should be undertaken, using the file paths given in the return pipeline_variables$return_files. After this has been completed, the final pipeline step, `windows_pipeline_quantification` should be run, giving the returned list from this function as input.

### Usage

    windows_pipeline_isoforms(pipeline_variables)

### Arguments

`pipeline_variables` | the list returned from `windows_pipeline_isoforms`.

### Value

the updated `pipeline_variables` list, with information required for the final pipeline step.

### Examples

    ## example windows pipeline for BULK data. See Vignette for single cell data.

    # download the two fastq files, move them to a folder to be merged together
    temp_path <- tempfile()
    bfc <- BiocFileCache::BiocFileCache(temp_path, ask=FALSE)
    file_url <-
        "https://raw.githubusercontent.com/OliverVoogd/FLAMESData/master/data"
    # download the required fastq files, and move them to new folder
    fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq1", paste(file_url, "fastq/sample1.fastq.gz", sep="/")))]]
    fastq2 <- bfc[[names(BiocFileCache::bfcadd(bfc, "Fastq2", paste(file_url, "fastq/sample2.fastq.gz", sep="/")))]]
    fastq_dir <- paste(temp_path, "fastq_dir", sep="/") # the downloaded fastq files need to be in a directory to be merged together
    dir.create(fastq_dir)
    file.copy(c(fastq1, fastq2), fastq_dir)
    unlink(c(fastq1, fastq2)) # the original files can be deleted

    # run the FLAMES bulk pipeline setup
    #pipeline_variables <- bulk_windows_pipeline_setup(annot=system.file("extdata/SIRV_anno.gtf", package="FLAMES"),
    #                   fastq=fastq_dir,
    #                   outdir=tempdir(), genome_fa=system.file("extdata/SIRV_genomefa.fasta", package="FLAMES"),
    #                   config_file=system.file("extdata/SIRV_config_default.json", package="FLAMES"))
    # read alignment is handled externally (below downloads aligned bam for example)
    # genome_bam <- paste0(temp_path, "/align2genome.bam")
    # file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Genome BAM", paste(file_url, "align2genome.bam", sep="/")))]], genome_bam)
    #
    # genome_index <- paste0(temp_path, "/align2genome.bam.bai")
    # file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Genome BAM Index", paste(file_url, "align2genome.bam.bai", sep="/")))]], genome_index)
    # pipeline_variables$genome_bam = genome_bam
    #
    # # run the FLAMES bulk pipeline find isoforms step
    # pipeline_variables <- windows_pipeline_isoforms(pipeline_variables)
    #
    # # read realignment is handled externally
    # realign_bam <- paste0(temp_path, "/realign2genome.bam")
    # file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Realign BAM", paste(file_url, "realign2transcript.bam", sep="/")))]], realign_bam)
    #
    # realign_index <- paste0(temp_path, "/realign2genome.bam.bai")
    # file.rename(bfc[[names(BiocFileCache::bfcadd(bfc, "Realign BAM Index", paste(file_url, "realign2transcript.bam.bai", sep="/")))]], realign_index)
    # pipeline_variables$realign_bam <- realign_bam
    #
    # # finally, quantification, which returns a Summarized Experiment object
    # se <- windows_pipeline_quantification(pipeline_variables)

[Package FLAMES version 1.0.2 Index]