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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.
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Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM