Tweet
I am planning to confirm the expression of my gene in a bacterial species based on RNA-seq data available in SRA. I am confused by how I should deal with it. Do I need to assemble the transcriptome first and then do blast search? Or is there any other way in which I can make sure that the gene is expressed without assembling the transcriptome? Thanks!
-
-
It depends on what information is available for the species you are working on: best case there is a reference genome and good annotation (GTF, GFF file on UCSC, Ensembl). Then you can align against the reference and use the GTF/GFF to determine number of reads at a particular feature (gene, exon) of interest, using HTSeq-counts or cufflinks for example.
"Do I need to assemble the transcriptome first and then do blast search?" If no reference genome/annotation exists you will need to do this, first assemble your transcriptome (plenty of tools out there) then align against it and blast for your sequence of interest. Are you looking for genes by orthology, or are they known in the species?
If you give more specific information people will give clearer and more detailed ideas about how to proceed.
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
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...04-22-2024, 07:01 AM
Comment