Question: Detecting differential isoforms in low expressed genes
0
gravatar for fatemehpeymani
17 months ago by
fatemehpeymani10 wrote:

Hi there

We are analyzing RNA-seq data of two patients and two control of a family with the causative mutation in a donor site. Miso and junction-seq couldn't detect differential isoform due to low expression of the causative gene. We have supposed that one of the exons has been skipped by the information in bam file but we are doubtful yet . Could anyone offer a software/package to detect differential isoform in low expressed genes?

rna-seq • 392 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by fatemehpeymani10
1

Thanks, I will try it out...

ADD REPLYlink written 17 months ago by fatemehpeymani10

Have you considered DEXSeq: Inference of differential exon usage in RNA-Seq ?

By the way, how low, exactly, is 'low'? If the other programs that you have used could not detect them, them neither, perhaps, can DEXSeq. In this case, you may want to considered lowering your thresholds when processing the data, such as minimum reads per isoform (if going by the StringTie (replaces TopHat) route) or by modifying some other threshold o raw counts (EdgeR and DESeq2).

Kevin

ADD REPLYlink written 17 months ago by Kevin Blighe46k
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