Hii, I am using Quantas method to identify splice variant in my data. I have single end RNA seq data on mouse brain. I am facing a problem regarding quantas command. To be more specific I used this command perl /home/kauranil/NGS_analysis/Quantas_files/Quantas/countit/summarize_splicing_wrapper.pl -v -big -conf /home/kauranil/NGS_analysis/Quantas_files/mm10/mm10.conf -dbkey /home/kauranil/NGS_analysis/Quantas_files/mm10/mm10 -cass -taca -alt5 -alt3 -mutx -iret /home/kauranil/NGS_analysis/OLego/17ca1.uniq.bed countit_out**
But I am getting this error separate genomic and junction reads ... analyze cass ... annotation of AS type cass does not exist at /home/kauranil/NGS_analysis/Quantas_files/Quantas/countit/summarize_splicing_wrapper.pl line 159.
Can anyone help me? Does anyone know how to analyze single strand RNA-Seq data for splice variant using olego and quantas?
Best, Lalit
