Tweet
I'm a beginner in RNAseq analysis (Illumina, PE reads). In FastQC, I got a failure on "Per base N content" towards the 3' end (95-99bp). I would expect quality score to drop here but the scores are above 32. Is this normal?
-
-
Can you post the plot? It is possible that a fraction (above the threshold) of the reads have N's in those positions. Those could be trimmed out. -
RNAseq fastqc - Failed "Per base N content"
Thanks GenoMax for your prompt feedback.
Here you have the plots.Comment
-
That is what I had thought (looks good otherwise). A bit of trimming should get rid of the N's. Most aligners will also soft-clip those N's if they are at the end of the reads.Comment
-
Nothing to worry about then? Thanks!Comment
-
Nope. Go ahead and trim the reads (lots of other threads on trimming programs).
Re-check FastQC afterwards and that "fail" should be gone.Comment
-
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 on Modified Bases...Yesterday, 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
Comment