Entering edit mode
5 months ago
Nham
•
0
Dear all,
Just starting out and excited to learn all about Sequencing. We did a abx time course for Gonorrhoea and have over 120 RNA seq Files (PE). I can do the basic RNA seq analysis and can find the DE genes (aim 1). My second aim is to find regions of the Gonorrhoea genome that are not transcribed using the RNA seq data. Thanking everyone in advance:-)
Your first aim seems pretty straightforward. Your second one not so much. Some transcripts will just amplify poorly or be lowly expressed and drop out of the sampling due to random chance. So not finding a transcript doesn't necessarily mean it's not being transcribed. I think other methods should be used in conjunction with RNA-seq for your second aim. Things like ATAC-seq are most suitable for finding transcribed/non-transcribed genomic loci.