Differential exon usage using RPM

Question

[rudnevav]

Dear all,

I am new to RNA-Seq analysis. I've obtained RNA-Seq data in wig format. Here is an example:

bedGraph section chr1:11624-117322

chr1 11624 11675 0.00551354 chr1 11680 11710 0.00551354 chr1 11710 11711 0.0110271

I have a list of genes for which I would like to find out if there is any difference in terms of exon usage between two conditions.

Would you have any tips on how to proceed with such analysis?

After some googling I came across the "DEXSeq" R package. Unfortunately, the manual does not explain how to use with the data in the format I have. Is this at all possible?

Many thanks!

Answer 1

[Devon Ryan]

I'm going to guess that this data is either from ENCODE or TCGA. In any case, the only thing you can reasonably do with this is perform visual inspection. You'll want to convert such files to bigWig format and then view them in IGV, paying attention to your gene(s) of interest. Perhaps you'll see vastly higher/lower relative signal in a few exons. Note that this is going to be qualitative, since data in this form isn't appropriate for statistical analysis (at least without knowing vastly more detail about how the analysis had been performed up to the point at which the files you have were created). In general, try to get either BAM or fastq files and start reanalysing things from there.

[rudnevav]

Thank you so much for the clarification!