[Bioc-devel] sensibility and specificity in trimLRpatterns

[Shepherd, Lori]

This is probably a better post on the support site so the broader community could answer.



https://support.bioconductor.org/




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Leandro Roser <learoser using gmail.com>
Sent: Wednesday, March 13, 2019 7:32:02 AM
To: bioc-devel
Subject: [Bioc-devel] sensibility and specificity in trimLRpatterns

Hello Bioc,

I am running some tests to compare trimLRpatterns vs other trimming
tools (skewer, cutadapt, AdapterRemoval).

I have generated simulated data using ART
(https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm).
In particular, there is a modified version of the program from the
authors of Skewer that allows to simulate the contamination with
adaptors (http://sourceforge.net/projects/skewer/files/Simulator/).

For my simulations, I have created reads of 150 bp for a coverage of
20x, and a fragment size of 200 bp +- 50 bp, to simulate the
contamination with adaptors in those reads with small fragment size.
The quality profiles were taken from actual MiSeq E.  coli Fastq
files.

Most of the programs achieve a sensibility/specificity of 99%.
trimLRpatterns is showing high specificity (99%) but a very low
sensibility (max. 16%), having problems to remove the adaptors
globally. I have changed different parameters, but I can't improve the
value.

Attached is a test script for a portion of the simulated data, where
I'm varying max.Rmismatch from 1 to 50.

I know exactly the length of the true trimmed reads, the location in
the genome is attached in the bed file. So, the width can be compared
with the output of the program. I am using the same statistics of the
AdapterRemoval paper.

 Any advice in relation to this?

Thanks!

Leandro


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