summary_stats_star: Get mapping summary statistics from STAR

View source: R/02_qc.R

summary_stats_starR Documentation

Get mapping summary statistics from STAR

Description

Get mapping summary statistics from STAR

Usage

summary_stats_star(star_dir = "results/03_read_mapping")

Arguments

star_dir

Directory where STAR .log files are stored. Default: results/03_read_mapping.

Value

A data frame with STAR summary stats for each sample containing the following variables (all numeric, except Sample):

  • Sample

  • total_reads

  • avg_input_read_length

  • uniquely_mapped

  • uniquely_mapped_percent

  • avg_mapped_read_length

  • num_splices

  • num_annotated_splices

  • num_GTAG_splices

  • num_GCAG_splices

  • num_ATAC_splices

  • num_noncanonical_splices

  • mismatch_rate

  • deletion_rate

  • deletion_length

  • insertion_rate

  • insertion_length

  • multimapped

  • multimapped_percent

  • multimapped_toomany

  • multimapped_toomany_percent

  • unmapped_mismatches_percent

  • unmapped_tooshort_percent

  • unmapped_other_percent

  • unmapped_mismatches

  • unmapped_tooshort

  • unmapped_other

Examples

star_dir <- system.file("extdata", package = "bears")
qc_table <- summary_stats_star(star_dir)

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.