summary_stats_star: Get mapping summary statistics from STAR

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

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.