Error when '5_utr_seq_similarity' and '3_utr_seq_similarity' used

[lananh-ngn]

Hello, I wanted to try '5_utr_seq_similarity' and '3_utr_seq_similarity' in consequencesToAnalyze for analyzeSwitchConsequences but it raised this error:

Step 1 of 4: Extracting genes with isoform switches...
Step 2 of 4: Analyzing 277 pairwise isoforms comparisons...
 |                                                                                                                                                |   0%Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'nchar': error in evaluating the argument 'x' in selecting a method for function 'gsub': unable to find an inherited method for function 'alignedSubject' for signature '"QualityAlignedXStringSet"'
Error: with piece 1: 
                    isoformUpregulated                 isoformDownregulated comparison
1 c8f41274-d697-427a-892b-4ab7e2dabe82 8d0b8594-5eaa-4554-adc7-60ea809b6d37          1

The error is not raised for other consequences tested. How can I fix this error? Thank you in advance, Best regards, Lan Anh

[kvittingseerup]

Thanks for reaching out 🙂

That does seem strange - and not like a problem I can re-create. Which version of IsoformSwitchAnalyzeR are you using? If you are not using > 1.17.03 could you try updating here from the GitHub, restart R and run the function again?

[lananh-ngn]

@kvittingseerup Thank you for your quick answer. Sorry for not mentioning it. When I used sessionInfo(), it shows that the version is 2.01.10.

[kvittingseerup]

Unfortunatly I cannot reproduce the error. Would you be willing to share yourswitchAnalyzeRlist with me? I would naturally keep it confidential and delete it after the issue was resolved?

If yes you can save the switchAnalyzeRlist (the list you give as input to analyzeSwitchConsequences) via the save() function and email it to me.

[kvittingseerup]

I think I found the problem. Please grap the newest version from github, restart R and try again (entire workflow).

[lananh-ngn]

Hello, sorry for the previous message if you received any notification. I downloaoded the latest version from github, restarted R and tried again but now when I use the workflow, I have less transcripts in my output than before which is confusing.

[kvittingseerup]

Please open a new issue since it is a new problem 🙂

Also you need to describe better what "less transcript means"