Detecting differential isoforms in low expressed genes

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6.7 years ago

fatemehpeymani ▴ 10

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 rna-seq • 1.1k views

ADD COMMENT • link 6.7 years ago by fatemehpeymani ▴ 10

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Thanks, I will try it out...

ADD REPLY • link 6.7 years ago by fatemehpeymani ▴ 10

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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 REPLY • link 6.7 years ago by Kevin Blighe 88k

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