Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am running target seq (illumina) with primers targeting only exon-exon junctions e.g. 1-2, 2-3, 3-4.. I am studying 1) exon skipping* and 2) intron retention of my sample.
I have run the usual RNA-Seq analysis protocol: FASTQ Groomer -> FASTQC -> Trimmomatic -> Top Hat -> Mpileup ->Varscan
But, i can't achieve the intended tasks. Any good recommendations?
*The exon skipping is expected to by partial event ( heterozygous splicing)
Thank you very much!!