It seems that the mainstream tools used for RNA-Seq analysis are Tophat and Cufflinks. However, since Tophat is bowtie-based it can't do gapped alignment with short reads. I thought of mapping with BWA and using the resulting SAM with Cufflinks, but as BWA is not meant for RNA-Seq alignment I am hesitant. Does anyone know of an RNA-Seq aligner that supports gapped alignment?
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Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.
Nucleic Acid Quality Control
Preparing for NGS starts with isolating the...-
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In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...-
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