Question: intron retention analysis
gravatar for kuick77
2.5 years ago by
kuick7710 wrote:

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!!

tophat galaxy • 686 views
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