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Why don't you give HTSeq-count a try? It takes a GTF file and a sam file as an input and outputs counts per gene for each gene in the GTF file.Leave a comment:
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GTF file with one line per gene?
I would like to use bedtools to extract raw gene counts from my .bam files. However, I was using UCSC_Genes.gtf (human) as my source file, but that file contains multiple lines for each gene, which is an issue since the output from bedtools is in the same format.
Where can I find a .gtf file containing only a single line for each gene? Preferably with Entrez gene IDs if this is easily available.
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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
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