Hello everyone, I have following questions:
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.
Thank you.
Welcome, @Mukaram_Bhat
We have transcriptomics tutorials here.
This is probably the best place to start for your first question.
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.
Hopefully this helps! 
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.
See the Deeptools tool group since I think it is what you are looking for. More → https://deeptools.readthedocs.io/
To pull in annotation tracks from UCSC, this tutorial is doing something else but has a good example of how to query the UCSC Table Browser – you could adopt this for other tracks they host. → Hands-on: From peaks to genes / From peaks to genes / Introduction to Galaxy Analyses. For other annotation sources, use the Upload tool.
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.
This topic has a screenshot → UCSC link using Galaxy to see RNA seq peaks - #2 by jennaj
UCSC hosts some model organisms, and those will have annotation from other sources, too. See the Help at UCSC for more. → https://genome.ucsc.edu/FAQ/
IGV needs to be installed but will allow you to create a new genomic backbone even if they do not have the pre-computed.