Full SCENIC Pipeline for chicken

[austinkunch]

Hi, I see there are Motif to TF annotations for Chicken in cistargetdb, but for Databases ranking the whole genome of the species, there is only data for human, mouse, fly. Does anyone know where I can find Feather files for ranking the whole genome of chicken to be used with the Chicken Motif to TF annotations (in pySCENIC)?

Also, I have batch effects in my data. Should I normalize and correct for batch effects before running data through the scenic pipeline, or pass the raw counts through the pipeline without normalization and batch effect correction?

Thank you!

[DiracZhu1998]

Hi, I see there are Motif to TF annotations for Chicken in cistargetdb, but for Databases ranking the whole genome of the species, there is only data for human, mouse, fly. Does anyone know where I can find Feather files for ranking the whole genome of chicken to be used with the Chicken Motif to TF annotations (in pySCENIC)?

Also, I have batch effects in my data. Should I normalize and correct for batch effects before running data through the scenic pipeline, or pass the raw counts through the pipeline without normalization and batch effect correction?

Thank you!

Hi Austin, I was wondering have you managed to solve that ? Thanks!