TOBIAS
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loosolab
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Hello, I understand that found motifs that have a p-value smaller than threshold p-value make it to the TF list, where they are assigned their footprint score. (TF motifs with...
Hi, this is probably a simple question, but can footprint regions still have peaks? I'm talking about a case such as this:  I wouldn't expect footprints to have this...
Hi, Thanks for this great tool. Is it possible to run Tobias on single-cell ATAC-seq data or clusters derived from single-cell data analysis? If there is any workaround possible that...
What are TFBS_score based on? Does the tool use TOMTOM or something similar? Is there any guideline for considering a good TFBS score to select only high confidence motif match?
Hi, Thank you for the tool and I know this is not an insightful question.. However, when I am reading into the configuration file of the sample TOBIAS pipeline, I...
Is it possible to run a genotype-treatment interaction type analysis for differential binding? Or, any intermediate data from Tobias pipeline that could be used for such analysis?
Hi, In the Tobias analysis, am at the BINDetect step and when I try generating plots I get plots that look very smooth. Generally, Tn5 cut sites are strong, even...
Hi, Thank you for your great tool. My reads (in the bam file) are already shifted. Is there a way to prevent ATACorrect from shifting them again? Can I just...
Is the "TOBIAS ATACorrect" suitable for DNase-seq where DNase I cut the chromatin?
Hi, I've been running TOBIAS for a while but have received an error that I've been running for the validation set that I did not get for my discovery set...
