Tweet
In the edgeR analysis, I utilized "total exon reads" as the raw counts. I am wondering if this is fine or not.
Thanks for any comments!
Thanks for any comments!
-
-
What is your biological question of interest ? -
I have two groups. Each group has two subgroups. Each subgroup has 8 replicates. I want to know the differential expression of genes within subgroup, between subgroup and among group.
Thanks!Comment
-
You sum the reads in all exons for each gene. That's a good approach. Some experimental protocols also get a lot of intronic reads because many RNAs weren't processed. This avoids that problem. Although it's still possible that in your cell type, the spliced structure of some genes be unannotated and novel. But, counting in exons is the simplest method to use.Comment
-
Thank you for the comments!Comment
-
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 -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
Comment