Can the input file only be filtered_feature_bc_matrix.h5? Or can it be changed to raw_feature_bc_matrix.h5?

[DoctorHDK]

Dear Author：
If users are analyzing an ST data set from 10X Visium platform, they only need to input "visiumPath".
Please make sure that "visiumPath" points to the standard output folder of 10X Space Ranger,
which has both (1) sequencing data, i.e., filtered_feature_bc_matrix.h5 file or filtered_feature_bc_matrix folder.
After filtering, the number of genes becomes smaller. I wonder if the raw data can be used to study the genes related to mitochondrial metabolism.
Hope to receive your reply. Thank you!

[beibeiru]

Hi, @DoctorHDK

Do you mean using the raw_feature_bc_matrix instead of the filtered output? To my understanding, the raw_feature_bc_matrix contains all detected spots (approximately 5,000), including both tissue-associated and background spots. In contrast, the filtered_feature_bc_matrix includes only spots that are identified as tissue-associated after Space Ranger processing.

Therefore, if you observe a smaller number of genes, it may indicate relatively low gene capture efficiency or sparse gene expression in the dataset.

Best,
Beibei