Hello,
I am trying to use the Kallisto aligner to run differential exon usage on my dataset. I want to run DEXSeq but am running into an error. Kallisto's GenomeBam does not include an NH tag so DEXSeq's dexseq_counts.py command refuses to run. When trying with Kallisto's PseudoBam the script reports them all as empty, likely due to the coordinates not matching up as PseudoBam doesn't project to genomic coordinates. I was wondering if there is some work around or changing dexseq_counts.py to not require the NH tag?
Thank you.
Thank you for your reply. That makes sense to me as I was thinking that kallisto's program seems to do the job of dexseq_counts.py. The papers you attached do mention using DEXSeq for some transcript analysis, however I do not seem to be able to get the DEXSeqDataSet to run. Would you happen to know which of the DEXSeqDataSet commands might take kallisto output (and in what form) and make it a DEXSeq object to be able to run through the DEXSeq command?
Thank you
So I have my tximport object from when I did DESeq2, and tried to run it through DEXSeqDataSet. The command said that it was a list not a dataframe/matrix so I pulled out just the counts that are in a matrix. However now I am getting an error that not all values in the assay are integers. Do you know if there is a way around this? all my attempts to change the numbers to integers just converts the matrix to an integer and leaves it useless and unable to convert back into a matrix.
Thank you.
You can do
round(counts)
to get a matrix of integers. Also note that if you previously did differential gene expression analysis with DESeq2, your count matrix is probably on the gene level. For DEXSeq, you need a transcript-level count matrix (i.e., by setting txOut=TRUE in the tximport call).I was able to get the command to work and got DEXseq to run for me.
Thank you very much.