Question: identifying indels/novel fusions in somatic tumor/normal transcriptome RNA-seq Illumina data
gravatar for genya35
16 months ago by
genya3510 wrote:


I’m a researcher trying to figure out the best way to analyze tumor + normal somatic transcriptome RNA-Seq fastq files obtained from Illumina by using tools on Galaxy. The goal is to discover and visualize novel fusions and mutation. I’m hoping to get advice from users here that have done similar analysis.

Here is what I’ve done so far:

  1. Ran FastQC
  2. Ran RNA-STAR to mapping to reference genome(hg19) with gtf(all chromosomes) with all default parameters.
  3. Ran Cufflinks on produced bam with the same gtf files. The output consisted of gene and transcript expression files.

Where do I go from here? Which files are the most helpful for identifying novel fusions? Do I filter the files to look only at transcripts/gene names that include Cuff* in the name? Should I also filter by highest PFKM values? How do I visualize/analyze normal and tumor output? How do I get a list of mutations (snvs,indels) present in the tumor files?

Should I use additional software for further analysis?

I would really appreciate a word of advice.

Thank you.

next-gen • 766 views
ADD COMMENTlink modified 16 months ago by Kevin Blighe41k • written 16 months ago by genya3510
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k wrote:

If you're using Galaxy and STAR, then use STAR-Fusion for identifying the potential fusion transcripts.

There is a tutorial specifically for this on here: Galaxy Workflow ' EGA VCaP RNA-Seq Fusion gene detection'

ADD COMMENTlink written 16 months ago by Kevin Blighe41k
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