I'm using Bowtie 1.0.1 to align paired-end ChIP-seq. At the end of alignment Bowtie reports the number of "reads processed" and in all cases it's about 5% higher than the actual number of reads in the fastq files I'm using as input. If I use the same fastq files and treat them as single-end reads the number of reported reads processed is correct. Any ideas what could cause this problem just when aligning paired-end reads?
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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