Error in Gene_Centric_Coding analysis about staarpipeline-tutorial HOT 5 CLOSED

Hi Pelin,

Thank you for your questions. For Gene_Centric_Coding analysis, have you prepared your genotype and annotation data into a single AGDS file one per chromosome, following the FAVORannotator steps?

Best,
Xihao

from staarpipeline-tutorial.

Hi Xihao,
Thank you for your quick response!

I have prepared the single aGDS file per chr by following your tutorial steps. I downloaded annotation data from FAVORannotator's database (containing 20 essential annotation scores) in CSV format​. However, it seems the problem is with some chunk chr files which are empty. Thank you made me notice! I will download again the FAVOR files and perform the analysis from the beginning.

Have a good day!
Bests,
Pelin

from staarpipeline-tutorial.

Hi Pelin,

You're very welcome. Before re-downloading the FAVOR files, could you please do a quick check for one of your aGDS file that caused the issue of

The GDS node "annotation/info/FunctionalAnnotation/genecode_comprehensive_exonic_category" does not exist

You may check this by pasting the output here using

library(SeqArray)
genofile <- seqOpen("/path_to_the_file/chr1.gds") # suppose chromosome 1 aGDS file has the issue above
genofile

Best,
Xihao

from staarpipeline-tutorial.

Dear Xihao,

I have checked each chromosome aGDS file as you suggested and there is no error, all of them are readable as formal class SeqVarGDSClass.

Bests,
Pelin

from staarpipeline-tutorial.

Hi Pelin,

Thanks for checking. In this case, could you please paste (1) the output of running the above 3 lines of scripts and (2) a screenshot of your Annotation_name_catalog file? This would help me better understand why genecode_comprehensive_exonic_category does not exist in your aGDS file.

Alternatively, you may send this information via email. Hope this helps.

Best,
Xihao

from staarpipeline-tutorial.