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Does anyone of any suggestions for RNA-seq quantitation tool using an referenced genome for illumina reads?
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Please have a look at this paper 'From RNA-seq reads to differential expression results' from Oshlack et al., 2010. Also consider adding Cufflinks and Scripture to Table 1.
Klaas -
RNA-seq quantitation
Cufflink which include cuffdiff can provide you the quantitation based on RPKM. DEseq and Seqmonk can also be useful.Comment
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Thank you for the suggestions, I think SeqMonk is the closest thing to what I am looking for, simple and basic; however it doesnt allow me to import my own annotated genome nor does it accept fastq files. Any other suggestions, I am continuing to look at other packages.
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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...Yesterday, 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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