Tweet
I'm using cuffdiff2 to examine the behavior of two paralogs in different maize haplotypes, and I've run into some output that isn't consistent withe previous data on these genes. qRT-PCR on these genes shows expression and Tophat alignments of single-end Illumina reads show expression as well. However, when I run cuffdiff2 on these files (2 biological replicates per haplotype), gene1 is assigned non-zero FPKM values and gene2 is assigned zero FPKM in all haplotypes. The quantification status for both genes is OK in all instances. I've had issues before with cuffdiff not recognizing annotated genes, creating novel transcripts where annotated models exist, etc., so I looked for a "novel" transcript at the same locus as gene2 but found nothing. I'm rather stymied at this point, and I'm curious if it sounds like I'm doing something wrong, others are having a similar problem, how to fix it, suggestions.
-
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