Tweet
When using bismark, if we set -I(min insert size) as 20, will sam file exclude overlapped reads? In my case 70% of pe reads in sam file are overlapped, though I set -I 20.
Is this normal?
Is this normal?
-
-
The latest version of bismark uses bowtie2, which has options for dealing with overlapping reads and by default can map mates that overlap. I am not sure if bismark uses the default for this or not, or whether or not this is one of the options available to adjust in Bismark. -
A following question is If I use bismark methylation call extractor for the overlapped pair end reads(count the overlapped CpG twice), will the same reads actually report two CpG calling in the same site?(I want to take advantage of this to check the accuracy of methylation calling)Originally posted by chadn737 View PostComment
-
See the --no_overlap option. I recall that, by default, it will report both. With the --no_overlap option, I recall it reporting the call from the first read in a pair. I wrote my own version that checks to see if the calls in overlapping reads are equivalent and found that they differ in ~0.01% of cases in a dataset that I checked. BTW, the accuracy of methylation calls in this case will be purely a function of the sequencing accuracy.Originally posted by serenaliao View PostComment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment