search

RJWANGbioinfo / APAlyzer

APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is the comparison of sequencing reads in regions demarcated by high-quality polyadenylation sites (PASs) annotated in the PolyA_DB database (https://exon.apps.wistar.org/PolyA_DB/v3/). The current version (v3.0) uses RNA-seq data to examine APA events in 3’ untranslated regions (3’UTRs) and in introns. The coding regions are used for gene expression calculation.
https://bioconductor.org/packages/release/bioc/html/APAlyzer.html
GNU Lesser General Public License v3.0
7 stars 4 forks source link

PAS2GEF errors out when processing small GTF file #9

Closed faricazjj closed 2 years ago

faricazjj commented 2 years ago

Hi,

I'm provided a small Gencode GTF file with ~500 lines that I'd like to use to obtain reference regions from for APAlyzer. The code I'm using is:

GTFfile="Mus_musculus.GRCm38.98.gtf.gz" 
PASREFraw=PAS2GEF(GTFfile)  
refUTRraw=PASREFraw$refUTRraw
dfIPAraw=PASREFraw$dfIPA
dfLEraw=PASREFraw$dfLE
PASREF=REF4PAS(refUTRraw,dfIPAraw,dfLEraw)

However, I'm getting the following error:

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'flesh' in selecting a method for function 'relist': subscript contains out-of-bounds indices
Calls: PAS2GEF ... normalizeSingleBracketSubscript -> NSBS -> NSBS -> .subscript_error
RJWANGbioinfo commented 2 years ago

@faricazjj thanks for the feedback, I will use this example file to check it

RJWANGbioinfo commented 2 years ago

@faricazjj , this issue is caused by the conflict between the annotator and GTF format in the previous version. It has been fixed now in the latest version. You can update your APAlyzer through:

BiocManager::install('RJWANGbioinfo/APAlyzer')

Then build the reference through using your GTF file:

GTFfile="gencode_2genes_Chr_prefix.vM18.annotation.gtf"
PASREFraw=PAS2GEF(GTFfile, AnnoMethod="V2")  
refUTRraw=PASREFraw$refUTRraw
dfIPAraw=PASREFraw$dfIPA
dfLEraw=PASREFraw$dfLE
PASREF=REF4PAS(refUTRraw,dfIPAraw,dfLEraw)
RJWANGbioinfo commented 2 years ago

close this ticket since it's fixed