How to generate the gtex_ctrl_db and tcga_matched_control_junction_count.h5ad, it is a good control.

[renyuan001]

I think that the control is the best. How to generate the gtex_ctrl_db and tcga_matched_control_junction_count.h5ad, Maybe a number of *.fasq in tcga and GTEx analysed by SNAF first?

[frankligy]

Yes we ran AltAnalyze on GTEx and TCGA matched control first to get the count junction matrix, then we convert them into h5ad file. I saved scripts I used for the conversion (https://github.com/frankligy/SNAF/tree/main/images/db_build).

For generating your own control dataset, you can follow other issues post (#34).

Thank you,
Frank

[renyuan001]

I want to use the both in the snaf.initialize step, and an error occured,

db_dir = '/home/ry-03/data/SNAF/data'
netMHCpan_path = '/home/ry-03/data/SNAF/netMHCpan-4.1/netMHCpan'
tcga_ctrl_db = ad.read_h5ad(os.path.join(db_dir,'controls','tcga_matched_control_junction_count.h5ad'))
gtex_ctrl_db = ad.read_h5ad(os.path.join(db_dir,'controls','GTEx_junction_counts.h5ad'))
add_control = {'tcga_control':tcga_ctrl_db,'gtex_ctrl':gtex_ctrl_db}
snaf.initialize(df=df,db_dir=db_dir,binding_method='netMHCpan',software_path=netMHCpan_path,add_control=add_control)
2024-05-12 19:15:40 starting initialization
Current loaded gtex cohort with shape (56692, 2629)
Adding cohort tcga_control with shape (54813, 705) to the database
now the shape of control db is (56999, 3334)
Traceback (most recent call last):
File "", line 1, in
File "/home/ry-03/miniconda3/envs/SNAF/lib/python3.7/site-packages/snaf/init.py", line 52, in initialize
adata = gtex_configuration(df,gtex_db,t_min,n_max,normal_cutoff, tumor_cutoff, normal_prevalance_cutoff, tumor_prevalance_cutoff, add_control)
File "/home/ry-03/miniconda3/envs/SNAF/lib/python3.7/site-packages/snaf/gtex.py", line 65, in gtex_configuration
assert len(set(control.var_names).intersection(tissue_dict.keys())) == 0
AssertionError

Maybe I need to filtered one by one, not together?

[renyuan001]

But it worked as:

add_control = {'tcga_control':tcga_ctrl_db}
snaf.initialize(df=df,db_dir=db_dir,binding_method='netMHCpan',software_path=netMHCpan_path,add_control=add_control)
2024-05-12 20:09:18 starting initialization
Current loaded gtex cohort with shape (56692, 2629)
Adding cohort tcga_control with shape (54813, 705) to the database
now the shape of control db is (56999, 3334)
2024-05-12 20:10:10 finishing initialization

[frankligy]

Yes, the reason is the same as this (#40), GTEx control is built in so you don't need to additionally add it, only TCGA control needs to be added as add_control.

[renyuan001]

Thank you so much for your patient and thoughtful answers.