Hi,
I ran both SCAPE and SCAPE-APA, and after obtaining the polyA sites, I used the provided annotation function to annotate them. However, while reviewing the annotation results, I noticed that some gene symbols assigned to the sites differed from those obtained using Cell Ranger. In my case, this discrepancy affected approximately 2,000 protein-coding genes and 7,000 non-coding genes.
After inspecting the R code, I found that the issue might stem from the use of different annotation sources—specifically, annotations derived from the GTF file and from the org.db package. Since I needed consistent gene symbols, I modified the code to resolve this inconsistency.
I’m wondering if you’ve encountered a similar issue before. Could this be due to differences in the version of org.db used (and which version of the org.db and gtf did you use)? Also, I’d like to understand if there was a specific reason for using two annotation sources instead of relying solely on the gene symbols provided in the GTF or GFF files.
Looking forward to your insights.
Best regards,
Qian
Hi,
I ran both SCAPE and SCAPE-APA, and after obtaining the polyA sites, I used the provided annotation function to annotate them. However, while reviewing the annotation results, I noticed that some gene symbols assigned to the sites differed from those obtained using Cell Ranger. In my case, this discrepancy affected approximately 2,000 protein-coding genes and 7,000 non-coding genes.
After inspecting the R code, I found that the issue might stem from the use of different annotation sources—specifically, annotations derived from the GTF file and from the org.db package. Since I needed consistent gene symbols, I modified the code to resolve this inconsistency.
I’m wondering if you’ve encountered a similar issue before. Could this be due to differences in the version of org.db used (and which version of the org.db and gtf did you use)? Also, I’d like to understand if there was a specific reason for using two annotation sources instead of relying solely on the gene symbols provided in the GTF or GFF files.
Looking forward to your insights.
Best regards,
Qian