I'd like to perform a search for possibly unidentified splicing variants of a specific protein in A. Thaliana. I do not have my own RNA-seq data. It has been suggested to me to use this workflow:
- Download RNA-seq data from SRA with
- Construct an index of reference sequences with
- Map the reads from RNA-seq data to the reference sequences with
- Remove non-specific mappings with
samtools view -q 10. Sort the mappings with
- Browse the aligned reads with
I have been given example data of another organism (not A. Thaliana) and have successfully completed these steps. However, I don't know how to apply that in my research. Specifically, I'd like to know:
- Is there other/better way to do do this?
- Can I narrow the search/alignment to a specifc gene?
- Where can I download A. Thaliana's reference genome in FASTA format?
- Which SRA runs should I choose for my analysis?
- How to interpret the results to get the information on the different splicing variants?
Linking a similar question I asked before: How to find an unidentified splicing variant of a protein?