generic_long_pipeline {FLAMES} | R Documentation

## Generic FLAMES pipeline

### Description

Generic implementation of the flames pipeline. Used for both bulk reads and single cell reads.

### Usage

    generic_long_pipeline(
      annot,
      fastq,
      in_bam,
      outdir,
      genome_fa,
      minimap2_dir,
      downsample_ratio,
      config_file,
      do_genome_align,
      do_isoform_id = TRUE,
      do_read_realign,
      do_transcript_quanti,
      gen_raw_isoform,
      has_UMI,
      MAX_DIST,
      MAX_TS_DIST,
      MAX_SPLICE_MATCH_DIST,
      min_fl_exon_len,
      Max_site_per_splice,
      Min_sup_cnt,
      Min_cnt_pct,
      Min_sup_pct,
      strand_specific,
      remove_incomp_reads,
      use_junctions,
      no_flank,
      use_annotation,
      min_tr_coverage,
      min_read_coverage
    )

### Arguments

`annot` | The file path to gene annotations file in gff3 format
`fastq` | The file path to input fastq file
`in_bam` | optional BAM file which replaces fastq directory argument. This skips the genome alignment and realignment steps
`outdir` | The path to directory to store all output files.
`genome_fa` | The file path to genome fasta file.
`minimap2_dir` | Path to the directory containing minimap2, if it is not in PATH. Only required if either or both of `do_genome_align` and `do_read_realign` are `TRUE`.
`downsample_ratio` | Integer; downsampling ratio if performing downsampling analysis.
`config_file` | File path to the JSON configuration file. If specified, `config_file` overrides all configuration parameters
`do_genome_align` | Boolean; specifies whether to run the genome alignment step. `TRUE` is recommended
`do_isoform_id` | Boolean; specifies whether to run the isoform identification step. `TRUE` is recommended
`do_read_realign` | Boolean; specifies whether to run the read realignment step. `TRUE` is recommended
`do_transcript_quanti` | Boolean; specifies whether to run the transcript quantification step. `TRUE` is recommended
`gen_raw_isoform` | Boolean; specifies whether a gff3 should be generated containing the raw isoform information in the isoform identification step
`has_UMI` | Boolean; specifies if the data contains UMI.
`MAX_DIST` | Real; maximum distance allowed when merging splicing sites in isoform consensus clustering.
`MAX_TS_DIST` | Real; maximum distance allowed when merging transcript start/end position in isoform consensus clustering.
`MAX_SPLICE_MATCH_DIST` | Real; maximum distance allowed when merging splice site called from the data and the reference annotation.
`min_fl_exon_len` | Real; minimum length for the first exon outside the gene body in reference annotation. This is to correct the alignment artifact
`Max_site_per_splice` | Real; maximum transcript start/end site combinations allowed per splice chain
`Min_sup_cnt` | Real; minimum number of read support an isoform. Decreasing this number will significantly increase the number of isoform detected.
`Min_cnt_pct` | Real; minimum percentage of count for an isoform relative to total count for the same gene.
`Min_sup_pct` | Real; minimum percentage of count for an splice chain that support a given transcript start/end site combination.
`strand_specific` | 1, -1 or 0. 1 indicates if reads are in the same strand as mRNA, -1 indicates reads are reverse complemented, 0 indicates reads are not strand specific.
`remove_incomp_reads` | Real; determines the strength of truncated isoform filtering. Larger number means more stringent filtering.
`use_junctions` | Boolean; determiens whether to use known splice junctions to help correct the alignment results
`no_flank` | Boolean; passed to minimap2 for synthetic spike-in data. Refer to Minimap2 document for more details
`use_annotation` | Boolean; specifies whether to use reference to help annotate known isoforms
`min_tr_coverage` | Real; minimum percentage of isoform coverage for a read to be aligned to that isoform
`min_read_coverage` | Real; minimum percentage of read coverage for a read to be uniquely aligned to that isoform

### Value

This generic function returns a named list containing the output file names of the provided output files in the given 'outdir' directory. These files are loaded into R in either a SummarizedExperiment or SingleCellExperiment object by the callers to this function, 'sc_long_pipeline()' and 'bulk_long_pipeline()' respectively.

[Package FLAMES version 1.0.2 Index]