TOBIAS
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loosolab
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Hi, Very impressive work with well documentation and ease of use. Even though this software is mainly aimed for ATAC-seq, this software may be also suitable for MNase-seq based assays?...
All columns are named as Site N, which is quite meaningless. Can anyone help to explain a bit? Or provide some instruction on how to show the network correctl in...
Hello, I am not sure how can I get the `.bed` file for `TOBIAS ATACorrect -p` Should I use a peak file of a single sample or should I merge...
Hi! First and foremost, thank you for developing and maintaining such an amazing tool. I have used TOBIAS to make a simple comparison between control cells and knockdown cells for...
Hi, I am trying to use TOBIAS in my ATAC-seq data, and I can't move forward with the create a TF network. I got the error below. Besides the bed...
Dear TOBIAS developers, Thank you for creating TOBIAS. I am having trouble using ClusterMotifs module. I get the following error msg when I tried using ClusterMotifs: Cmd used :ClusterMotifs --dist_method...
Hi, thanks for the remarkable job! I am currently exploring the creation of motif logos in the context of sequence motif analysis and have encountered some uncertainties. My initial understanding...
"I encountered this error while performing the analysis, how should I troubleshoot it? ``` Traceback (most recent call last): File "/home/yanghj/miniconda3/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds))...
Hi, How was the impressive Figure 2 in your original TOBIAS manuscript generated? It is a very clear way to examine progression of binding sites etc.. 1. Was this all...
