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Bedtools documentation states that one can add two extra fields to a bedpe file when using bamtobed. Does anyone know how to do that? I need to add the read sequences. Thanks.
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one possible solution is to use your bed output in conjunction with
bedtools getfasta -tab
then parse the output to get the bed formatting back by perl -wpl -i.bak -e 's/:|-/\t/g;'
if you need the reads themselves and not the genome sequence where they mapped, you could write a sam parser to simply print some of the columns of the sam file. all the info you need is in the sam, just need to look at the sam docs to figure out what you want to print (i.e. which columns) and how to modify the sam to get bed-like coordinates. awk is good for such a task, just be aware of the strand
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...Today, 07:11 AM -
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
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