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I have done an alignment and used the -H option to dump the multiple hits as well as the -u option to dump the reads that do not map. However, after the alignment, I was interested in getting the numbers of hits in each category (# unique mapping reads, # reads that map to multiple places, and # reads that do not map). I converted the 'map' file to a 'txt' file and counted the number of lines (I got 8,335,894) and then I counted the lines in the non-mapping file (I got 4,575,039). However, this totals to the total number of reads that I started with (12,910,933)! What goes in the multi mapping file? I unzipped it, but cannot discern the format at all. Do the reads that map to multiple positions also go on the 'map' file?
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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