8000 BINDetect output · Issue #311 · loosolab/TOBIAS · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

BINDetect output #311

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
apal6 opened this issue Mar 17, 2025 · 6 comments
Open

BINDetect output #311

apal6 opened this issue Mar 17, 2025 · 6 comments
Assignees
@hschult

Comments

@apal6
Copy link
apal6 commented Mar 17, 2025

Hi Tobias team,

I ran the TOBIAS BINDetect function on my samples but my plots folder is empty for each sample. I am not sure why that is happening when my slurm job finished successfully. I get the following outputs:

Image

What do you think could be going wrong?
command used:

TOBIAS BINDetect --motifs /ATAC-seq/external_data/JASPAR2024_CORE_non-redundant_pfms_meme.txt \ --signals /ATAC-seq/results3/bwa/merged_replicate/tobias_footprinting_results/ATACorrect_test/sample1/footprint_score/sample1.bw \ --genome /ATAC-seq/results3/genome/genome.fa \ --peaks /ATAC-seq/results3/bwa/merged_replicate/macs2/narrow_peak/sample1.mRp.clN_peaks.narrowPeak \ --outdir /ATAC-seq/results3/bwa/merged_replicate/tobias_footprinting_results/BinDetect_sample1

Thank you!
@hschult hschult self-assigned this Mar 18, 2025
@hschult
Copy link
Collaborator
hschult commented Mar 18, 2025

Hi @apal6

There is nothing wrong with your command. Can you provide more information? Do you have log files? It may also be an issue related to your data. Please try to do the test run, which you find here (test-data). You can try to load the files in IGV. I found that it often helps to understand the problem.

Best wishes
Hendrik

@apal6
Copy link
Author
apal6 commented Mar 18, 2025 •
edited
Loading

No, I actually don't have the log files. It just finished running without any errors. I am running it again, hopefully will get the output soon and can share the log files.

But I actually have a few doubts-

I have 4 samples. I want to run the tobias BINDetect in two samples (treatment1 vs treatment2)

I merged the narrowpeak files:

cat treatment1.mRp.clN_peaks.narrowPeak treatment2.mRp.clN_peaks.narrowPeak | sort -k1,1 -k2,2n | bedtools merge -i - -c 4,5 -o distinct,max > merged_peaks_with_info.bed

I then run the TOBIAS ATACorrect on each of the samples. Following that i run the footprint scores on each sample using the signal flag and then take the output to run TOBIAS BINDetect where --signal has both treatment1 and treatment2 and
--peaks has the merged_peaks_with_info.bed file.

TOBIAS BINDetect --motifs /ATAC-seq/external_data/JASPAR2024_CORE_non-redundant_pfms_meme.txt \ 
--signals /ATAC-seq/results3/bwa/merged_replicate/tobias_footprinting_results/ATACorrect_test/sample1/footprint_score/treatment1.bw /ATAC-seq/results3/bwa/merged_replicate/tobias_footprinting_results/ATACorrect_test/sample1/footprint_score/treatment2.bw  \ 
--genome /ATAC-seq/results3/genome/genome.fa \ 
--peaks /ATAC-seq/results3/bwa/merged_replicate/macs2/narrow_peak/merged_peaks_with_info.bed \
 --outdir /ATAC-seq/results3/bwa/merged_replicate/tobias_footprinting_results/BinDetect_merged_t1andt2

I am hoping to get this kind of volcanoplot

Image

Is it the correct way to do the combined analysis?
Thank you!

@hschult
Copy link
Collaborator
hschult commented Mar 25, 2025

If you want to compare conditions but have multiple samples per condition, you must merge the samples of each condition as a first step. Then you can go ahead with the steps as you described.

That being said, I recommend using our TOBIAS snakemake pipeline. It provides a full TOBIAS analysis while saving you the time it would take to do each step manually.

@apal6
Copy link
Author
apal6 commented Mar 26, 2025 •
edited
Loading

Hi @hschult, thank you. I did merge the two samples I want to compare and then ran the whole pipeline. I got the output but now i am trying hard to understand the output as both the conditions are showing similar output. here's an example:

Control aggregated signal:

Image

treated aggregated signal:

Image

However, from the RNA-seq analysis I did, i found this TF to be enriched only in the treated group. But here, I am seeing the signal in the control sample too. Not sure what is happening.
Additionally, I also saw some TFs to be opposite (enriched in control) even after specifying the treated sample first in the --signals flag. here's the code:

TOBIAS BINDetect --motifs /ATAC-seq/JASPAR2024_CORE_non-redundant_pfms_meme.txt \ --signals 2 treatment.bw control.bw \ --genome /genome/genome.fa \ --peaks merged_peaks.bed \ --outdir BinDetect_out

Can you help?
Thank you!

@github-actions GitHub Actions
Copy link

No activity for at least 30 days. Marking issue as stale. Stale issues are closed after one week.

@github-actions github-actions bot added the Stale label Apr 26, 2025
@hschult
Copy link
Collaborator
hschult commented Apr 29, 2025

Hi @apal6,

Please excuse the delayed answer.
Observing the FP in both of your conditions, despite the transcriptome telling you that the TF is not expressed, could hint at some kind of compensation. If you look at the JASPAR database, you'll find that it is common to have groups of TF with similar motifs. ATAC relies on the motif to predict which TF might be bound. So a TF with a similar motif might have bound in your treated condition.
I'm not sure what you mean by changing the order of the --signals flag. This shouldn't have an effect on the results; only the order of conditions should be affected in plots, tables, etc..

@github-actions github-actions bot removed the Stale label Apr 30, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@hschult hschult

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@hschult @apal6
0