My client has run targeted RNA sequencing for a list of genes from different chromosomes in human and wanted to perform alternative splicing analysis. I have never been working on these type of targeted data analysis and am wondering whether there is standard ways for this analysis. What programs I can use to do this analysis? Could somebody can give me some possible description of the procedure?
Check out previous posts
Or if your are newbie try this workflow,
Are those total RNA (Transcriptome) sequencing samples? If so,
1) FastQC (Check quality of sequencing).
4) SAMstat (Check quality of alignment)
7) GeneSCF v1.1 (command-line)/Enrichr (Web-based) [Gene ontology or pathway analysis for differentially expressed isoforms related genes, this step is only applicable for protein coding genes]. GeneSCF is more reliable than other tools because it is real-time based and also check other advantages of using GeneSCF.