User: j2h2k2

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j2h2k20
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Posts by j2h2k2

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Comment: C: Kallisto output with DEXSeq
... I was able to get the command to work and got DEXseq to run for me. Thank you very much. ...
written 13 months ago by j2h2k20
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Comment: C: Kallisto output with DEXSeq
... 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 kno ...
written 13 months ago by j2h2k20
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Comment: C: Kallisto output with DEXSeq
... 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 ...
written 13 months ago by j2h2k20
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Kallisto output with DEXSeq
... 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 repo ...
dexseq kallisto nh_tag written 13 months ago by j2h2k20 • updated 13 months ago by Alejandro Reyes1.7k

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