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analyzeCPAT uORF analysis

Hello! I have some novel transcripts and I want to use analyzeCPAT function of IsoformSwitchAnalyzeR pachage I described fully how I got the data here

I got cpat file by running

!cpat.py -g transcripts.fasta -d Human_logitModel.RData -x Human_Hexamer.tsv -o output1

I downloaded the full tsv file (output1.ORF_prob.tsv)

I tried running analyzeCPAT with those data, but got an error

analyzeCPAT(switchAnalyzeRlist = aSwitchList,
            pathToCPATresultFile = "output1.ORF_prob.tsv",
            codingCutoff = 0.725,
            removeNoncodinORFs = T)

Error in analyzeCPAT(switchAnalyzeRlist = aSwitchList, pathToCPATresultFile = "output1.ORF_prob.tsv", : There seems to be a problem with the CPAT result file. Please check it is the rigth file and try again

How can I fix it?

r isoformswitchanalyzer uorf analyzecpat
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written by Sarah • Sarah

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