Tweet
Does anyone have decent strategy for taking isotigs.fna (cDNA sequences) and outputting a list of non-redundant isotigs that could be used for mapping rnaseq reads for differential expression analysis. I suspect I am losing about 50% of my illumina reads during mapping because they do not map uniquely.
-
-
I guess one option would be to assemble illumina and 454 together in newbler with the -rip option and then to parse the ACE file. However I have ~90 million 100-bp HiSeq reads and so a hybrid assembly isn't possible on our hardware.
Apologies I just realised -rip doesn't work in cDNA mode. -
I heard somebody using CAP3 with the assembled isotigs as input and a single transcript (variant) per gene as output. But, you will anyways get splice variants. Aren't there any programs out there to map RNAseq reads that take splice variants in the reference into account?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