Entering edit mode
18 months ago
Sarah
•
0
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?