Finding fused-transcripts from an expression matrix

Question

[VolEr]

Hi,

I am interested in finding transcript fusions in Treehouse compendium of RNA-Seq gene expression data from tumors - GSE129326. But, GEO provides only its expression matrix and metadata, nothing more. I am wondering if there is a way to utilize these files to carry out Star-Fusion or something similar in R or Galaxy platform. I couldn't locate the FASTQ files, but they say that data were processed as follows: Adapters are removed with CutAdapt v1.9 ​​ Reads are aligned by STAR v 2.4.2a using indices generated from the human reference genome GRCh38 and the human gene models Gencode 23 RSEM 1.2.25 is used to quantify gene expression​. Gene level expression in TPM is log transformed: log2(TPM+1)

Thank you in advance for your comments.

Answer 1

[ATpoint]

No. Fusion gene detection does not work with a count matrix. You need to get the raw data from SRA and then use assembly- or alignment-based strategies.

[VolEr]

Thank you ATpoint for your reply. I agree but just wanted to ask in case you may know another way to get it around. Unfortunately, SRA doesn't have raw data, it's more likely due to the size of numerous different RNA-seq datasets combined as Treehouse compendium.