pinellolab/dictys

Run bulk ATAC-seq data failed!!!

Closed this issue · 5 comments

bioinformaticspcj commented

Dear Lingfei,

I have tried to add the number to distinguish each motif name as you suggested in #28. However the same error still occured. I also tried dictys_helper makefile_check.py -c command, the results are as follows:
Joint profile: True
Found 7047 cells with RNA profile
Found 55095 genes with RNA profile
ERROR:root:2
WARNING:root:Using RNA cell names for ATAC cell names for validations below.
Found 7047 cells with ATAC profile
Found 356 motifs
Found 356 TFs
Found 311 TFs in current dataset
Missing 45 TFs in current dataset: ANDR,AP2A,AP2C,ARI5B,BHA15,BHE40,BMAL1,BRAC,COE1,COT1,COT2,DMRTB,EVI1,GCR,HEN1,HNF6,HTF4,ITF2,KAISO,NDF1,NDF2,NGN2,NKX2-8,PEBB,PKNX1,PRD14,PRD16,PRGR,RORG,SUH,TF2L1,TF65,TF7L1,TF7L2,TFE2,THA,THA11,ZBT17,ZBT7A,ZKSC1,ZN143,ZN281,ZN322,ZN335,ZN431
Found 268 genes with TSS information
WARNING:root:Cannot find dynamic.mk or traj_node.h5. Skipping dynamic network inference checks.
Traceback (most recent call last):
File "/data/nfs/OriginTools/pcj/python3/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/helper/makefile_check.py", line 354, in
raise RuntimeError(f'Found {nerr} error(s) in total.')
RuntimeError: Found 1 error(s) in total.

The motif file that I used has been uploaded to https://figshare.com/articles/dataset/Mouse_TF_motif/24333844 in figshare.

Could you spare sometime to help me?

Thanks a lot.

Best,
Bob

lingfeiwang commented

Dear Bob,

That seems alright for bulk ATAC-seq data assuming you followed #23, because

Expect failures in "Validate input data" step because of that and stop before "Network inference" step.

Btw if you update Dictys to the latest version you should see the error message showing up correctly.

Please let us know if you have further questions.

Lingfei

bioinformaticspcj commented
lingfeiwang commented

Dear Bob,

Thank you for the clarifications. Could you update Dictys to the latest dev branch and run the same line for GRN inference again? It should provide expanded error message about which motif names are duplicates. From this we can troubleshoot further.

Lingfei

bioinformaticspcj commented
lingfeiwang commented

It appears that a motif with empty name '' was identified. Is it because you have an empty line in the end of your motif file?

I also suggest to try the tutorial first. If the tutorial doesn't work for you, please raise an issue.

If the tutorial works, you can try changing the motif file to your own one. You can also try many things like using only one motif or splitting the motif file by half to see where the problem is. You can try your motif file with homer too. But generally, motif files are an established format and you can search for ways to diagnose any problem with it.