I want to check the overall splicing in my RNA seq data, is it possible to check or visualize it.
I am interested in one gene and want to see what are the transcription factors that go and bind in the promoter of that gene. I have RNA seq data in bam and bigwig formats. Is it possible to check the transcription factors specifically in my dataset.
For your second question, you could explore your data in the UCSC genome browser. Try the ENCODE annotation tracks. You could put everything into a session to save it and add more annotations (including custom tracks from your Galaxy analysis). See the “My Data” tab at the top https://genome.ucsc.edu/ or start with the trainings they offer here https://genome.ucsc.edu/training/index.html.
Thank you, Jennifer, for the response. Can you expand on my second question? What are custom tracks? I do have bam and bigwig files (that i have from RNA Seq data). How it can help me to know the transcription factors that bind specfically to the promoter of interest? Also, can you please guide me step by step how i can upload the files in UCSC broweser and analayze the promoter region visually.
These are big questions – I hope this covers what you want to know!
A custom track is an genomic feature track that you create yourself. That can be the original bam or bigwig files, or any that you create by exploring intersections of your data with other annotation tracks.
Data can be visualized at IGV, IVG, and UCSC. The fasta index, aka “database” assigned to your dataset is the link. If you click on the visualize icon in your dataset, the applications you can send your data to will be listed.