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 complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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