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.
I am trying to run PASEXP_3UTR with paired end reads and get the following error:
It says that the library is single end, and I checked the code and found APAlyzer.R line 37 that the parameter singleEnd is hardcoded to TRUE.
Not sure if I'm missing anything but how do you suggest for me to go ahead and run PASEXP_3UTR with paired end read? Did I miss any parameter that I should be setting to run paired end reads?
Hello Ruijia,
I have the same question as the person above. Additionally, how is the "strandtype" assigned to R1 or R2 of paired-end files? For example, I know that for my data, the "R1" should be "strandtype=invert".
Thanks!
SMM02
commented
1 year ago
Hi Ruijia,
I am trying to run PASEXP_3UTR with paired end reads and get the following error:
It says that the library is single end, and I checked the code and found APAlyzer.R line 37 that the parameter singleEnd is hardcoded to TRUE.
Not sure if I'm missing anything but how do you suggest for me to go ahead and run PASEXP_3UTR with paired end read? Did I miss any parameter that I should be setting to run paired end reads?