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I used kallisto genomebam to perform pseudoalignment on stranded single-end and paired-end data and generated bam files. I visualized my bam files on IGV and compared them to the counts I got from kallisto/tximport and they don't match up. Sometimes my count would say 0 but I see reads on IGV or it says there are thousands of reads but I don't see anything on IGV. Has anyone else encountered this issue and resolved it? Also what does the direction of the reads indicate? I have reads that go in the same and opposite direction as my genes. Also, for my stranded paired-end data, why do I have LR and RL reads? I was reading that RL means duplication or translocation; is that always the explanation?
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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...04-22-2024, 07:01 AM -
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...04-04-2024, 04:25 PM