feature_file_editor: Prediction and annotation of sRNAs and UTRs from RNA-seq data

In irilenia/baerhunter: Detection and Analysis of Expressed Intergenic Elements in Bacterial RNA-seq Data

Prediction and annotation of sRNAs and UTRs from RNA-seq data

Description

A wrapper function that executes all prediction steps for each strand and builds the final GFF3 annotation.

Usage

feature_file_editor(
  bam_directory = ".",
  bam_list = "",
  original_annotation_file,
  annot_file_dir = ".",
  output_file,
  original_sRNA_annotation,
  low_coverage_cutoff,
  high_coverage_cutoff,
  min_sRNA_length,
  min_UTR_length,
  paired_end_data = FALSE,
  strandedness = "stranded"
)

Arguments

bam_directory	The directory containing BAM files.
bam_list	Optional newline separated text file of filenames of bam files. File must be located in bam_location directory.
original_annotation_file	GFF3 genome annotation file.
annot_file_dir	The directory containing the GFF3 annotation file.
output_file	A string containing the name of an output file.
original_sRNA_annotation	A string indicating how the biotype of pre-annotated ncRNA, which can be found in the attribute column.In case if the user does not know how the sRNA is annotated, it can be set as "unknown". In this case, all RNAs apart from tRNAs and rRNAs will be removed from the selection.
low_coverage_cutoff	An integer indicating the low coverage threshold value.
high_coverage_cutoff	An integer indicating the high coverage threshold value.
min_sRNA_length	An integer indicating the minimum peak width/sRNA length.
min_UTR_length	An integer indicating the minimum UTR length.
paired_end_data	A boolean indicating if the reads are paired-end.
strandedness	A string outlining the type of the sequencing library: stranded, or reversely stranded.

Value

Outputs a new GFF3 file populated with predicted sRNAs and UTRs.

irilenia/baerhunter documentation built on May 18, 2024, 11:56 p.m.