will the bam files mapped from Ensembl index be ok to do featurecount with mm10

Question

[Kai_Qi]

Hi:

Today, I suddenly realized that I have been using Emsembl index to do mapping while when do the feature counting I turn to FeatureCounts in Rsubread using the in-built mm10 because it does have GRCm38. Obviously, the annotations are different, but will that affect the accuracy of results?

Thank you very much,

[GenoMax]

If chromosome names don't match then no, which is going to be the case here. Use Ensembl GTF to do the counting.

[Kai_Qi]

Thank you so much for clarifying. I notice the differences on the successfully assigned alignment:

Successfully assigned alignments : 31662019 (33.6%)

Previously I used the in-built annotation it is 60%-70%. Is this normal?

Thank you so much.

[Kai_Qi]

I find the reason. It is depends on what feature I am using to count. Sorry for being naive. I would like to keep the notes here.