BaseComposition: Identify polyA motif and/or polyA stretches from provided...

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Identify polyA motif and/or polyA stretches from provided genomic coordinates

Description

chrom <- chr8

Usage

BaseComposition(
  genome = NULL,
  chrom = NULL,
  start = NULL,
  stop = NULL,
  strand = NULL,
  coord = NULL,
  offset = -50,
  length = 250,
  mismatch = 1,
  AT_length = 13
)

Arguments

genome	genome object of organism.
chrom	chromosome
start	Upstream start position
stop	downstream end position
strand	'+' or '-'. This will define the applied direction of offset
coord	coordinates
offset	The
length	How many nucleotides of DNA sequence to return
mismatch	: The max number of mismatches allowed in poly A/T stretch (default 1)
AT_length	: length of A/T to search for within input sequence (default 13)

Details

start <- 70331172

stop <- 70331574

strand <- "+"

You need to run the following code: genome <- GenomicFeatures::makeTxDbFromGFF(gtf_file, format="gtf")

annotationType can be c("any", "start", "end", "within", "equal"),

Value

a dataframe with appended columns containing annotation

chrom <- 'chr16' start <- 49896378 stop <- 49911102 strand <- '+' genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

# Tmem126a intronic peak that coincides with a poly(A) rich region. chrom <- 'chr7' start <- 90451180 stop <- 90451380 strand <- '-' output <-BaseComposition(genome=genome, chrom=chrom, start=start, stop=stop, strand=strand)

# Dync1h1 intronic peak that coincides with a long poly(T) rich region coord <- "chr12:110609400-110609800:1" output <-BaseComposition(genome=genome, coord=coord)

TO DO: * If peak falls at end of exon then need to obtain sequence from next exon. This would require passing exon junction information.

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.