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 <[email protected]> on behalf of Leandro Roser <[email protected]> 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 This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
