Cannot import CPAT

[ElvaWong]

Hi, I have a problem importing external file from CPAT analysis. I want to import them to the SwitchList that underwent the isoformSwitchAnalysisPart1.

Here are some contents of my external files (all in TSV file format):

1. CPAT ID mRNA ORF_strand ORF_frame ORF_start ORF_end ORF Fickett Hexamer Coding_prob ENSMUST00000162751.8_ORF_1 3030 + 3 219 1931 1713 1.0091 0.105940749047772 0.999913680566869 ENSMUST00000162751.8_ORF_2 3030 - 1 369 1 369 0.7696 0.0566954545960345 0.271282579045262 ENSMUST00000162751.8_ORF_3 3030 + 1 1813 2016 204 0.9462 0.00327711877859152 0.112167274498432 ENSMUST00000162751.8_ORF_4 3030 + 1 1309 1509 201 0.992 0.106113544331737 0.170114280417295

# Here are errors that I got:
# Importing CPAT file
SwitchList_analyzed.p1_externel <- analyzeCPAT(
+     switchAnalyzeRlist = SwitchList_analyzed.p1,
+     pathToCPATresultFile = "C:/Users/elvag/Desktop/Research_Practice/Linux/CPAT_output/CPAT_output.ORF_prob.tsv",
+     codingCutoff = 0.44,
+     removeNoncodinORFs = TRUE   # because ORF was predicted de novo
+ )
Error in analyzeCPAT(switchAnalyzeRlist = SwitchList_analyzed.p1, pathToCPATresultFile = "C:/Users/elvag/Desktop/Research_Practice/Linux/CPAT_output/CPAT_output.ORF_prob.tsv",  : 
  There seems to be a problem with the CPAT result file. Please check it is the rigth file and try again

[MustafaElshani]

Use CPAT2 instead of CPAT3

[chunxubioinfor]

@ElvaWong Hi Elva, sorry for the inconvenience. For this version, IsoformSwitchAnalyzeR only supports the CPAT2 analysis. So we recommend you to use old version or web server of CPAT. Thank you for your feedback! And we will try to update to be compatible with CPAT3 :)