What is the recommended workflow in Galaxy for analyzing RNA-seq data, specifically focusing on splice variants? Additionally, how can one convert BAM files to BigWig format using Galaxy?
If you are completely new to Galaxy, the first two tutorials here are a good place to start → Introduction to Galaxy and Sequence analysis
Then, move on to one of the introduction tutorials in the GTN Transcriptomics tutorials. Galaxy Training! If those are not quite what you want to do, it is still probably worth going through them to learn the basic steps with exact instructions, then you can explore the others.
For the conversion, search the tool panel with the datatype to find the options at the server where you are working. bamCoverage is a good general choice.
Thank you Jennifer! Actually I am trying to pick up the upregulated variant from the pool of variants of one gene. I processed my raw RNA seq data which was in fastq format to bam files then I choose view in igv. In igv i can see the peak across specific exon which aligns with a set of variants. Now I want to exactly which exon and which variant is giving a spike. Is it possible?
Also can we access the spikes let’s say I have a spike and it comes under exon1 now when I go into the Req seq i see there are multiple variants under this spike which comes under exon1. How to see which variant it is actually that shows spike under exon1?
Do you want to filter the VFC based on coordinates? Tool = VCF-BEDintersect
Thankyou Jennifer for response.
Currently working with splice variants in bigwig format, I received a suggestion to use VCF-BEDintersect for coordinate-based filtering of VFC. Could anyone guide me through the workflow or steps involved in utilizing this tool to analyze splice variants effectively?" or can you suggest me some video tutorial or maybe provide a reference? Thank you