IsoformSwitchAnalyzer is not accepting CPAT result file

Question

[Claire]

Dear All

I am using isoformswitchanalyzer smoothly till the part2 analysis which relies on some external databases. I got the results of CPAT successfully, CPAT output file I used to pass to isoformswitchanalyzer is cpat_ORF_prob.tsv and it looks like:

ID mRNA ORF_strand ORF_frame ORF_start ORF_end ORF Fickett Hexamer Coding_prob ENST00000341426.9_ORF_1 3235 + 1 223 1563 1341 1.3069 0.497437023084147 0.999999505977413 ENST00000341426.9_ORF_2 3235 + 3 426 677 252 1.3192 0.0868603323115237 0.47204435186642 ENST00000341426.9_ORF_3 3235 + 1 1774 1962 189 0.6174 -0.104404126218791 0.0121687485631606

I got this error:

[1] "Isoform Switch Identification, ORFs, ntSequence, aaSequence, Intron Retentions" Error in analyzeCPAT(mySwitchList, "cpat.ORF_prob.tsv", removeNoncodinORFs = TRUE, : There seems to be a problem with the CPAT result file. Please check it is the rigth file and try again Execution halted

Any help?

Thank you

Answer 1

[Kristoffer Vitting-Seerup]

Did you look for similar CPAT problems at the google group or GitHub?

[Claire]

I will take a look, thanks.