cluster_reads: Clustering anchor reads, sequencing reads passing a threshold...

In ctl43/TranSpotteR: Pipeline for identifying LINE1 insertoin in the WGS data

Clustering anchor reads, sequencing reads passing a threshold of mapping quality (MAPQ).

Description

Anchors, reads with sufficiently high mapping quality (e.g. MAPQ > 10) are clustered together.

Usage

cluster_reads(total, anchor_min_mapq, min_cov = 5, size_tol = 0, max_reads = 100)

Arguments

total	A GRanges object, imported from import_files, containing all the extracted sequence information.
anchor_min_mapq	A integer specifying the minimum mapping quality score for being a anchor reads.
min_cov	A integer specifying the minimum coverage that a cluster should have.
max_reads	A integer specifying the maxium reads that a cluster can have for reducing the computational cost at the later step, especially, read assembly.

Details

Here is an example of min_cov=3, 1112221112211111 (min_cov = 2) 1122333222111 (min_cov >= 3) ——– ———– —— <- filtered ——- <- included ——- ——

Value

A GRange object with a DataFrame that contains the reads consisting the cluster and their partner reads.

Author(s)

Cheuk-Ting Law

ctl43/TranSpotteR documentation built on Sept. 9, 2022, 5:49 p.m.