Psichomics Suppa Input issue
Entering edit mode
noahhelton98 ▴ 10
Last seen 8 months ago

Hi All,

I am looking to analyze differentially retained U12 introns across RNA-seq samples. To do this, I annotated the alternative splicing event "RI" using SUPPA2: generateEvents -i input.gtf -f ioe -e RI -o iPSCTLS2

I did this for all of my samples and to analyze I planned to use psichomics. However, when running the R code prepareAnnnotationsfromEvents, I got this error:

Error in order(events$Event type, events$Chromosome, events$Constitutive exon 1 start, : argument 5 is not a vector

Here is the code I used:

suppaOutput <- 'Suppa_Files/ioe'

suppa <- parseSuppaAnnotation(suppaOutput, types = 'RI', genome = 'CTL')
annot <- prepareAnnotationFromEvents(suppa)

Any suggestions to get this to work?

psichomics SUPPA Splicing Alternative Splicing Retained Introns • 140 views

Login before adding your answer.

Traffic: 388 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6