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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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Lineplot for specific transcription factor #236

Closed konsta-kukkonen closed 1 year ago

konsta-kukkonen commented 1 year ago

Hello!

Thank you for the software, it is very useful. I'm working with ATAC-seq data of a cell line with overexpression of a transcription factor. When doing the differential motif analysis with rgt-hint differential, the output of WT vs OE cells didn't include the lineplot for this transcription factor, although it is included to the motif database.

Is there a module for making the lineplot for specific transcription factor? And what would be the parameters it takes? rgt-hint plotting, sounds like it might be the one, but it does not have very comprehensive usage instructions. What would be the input, for rgt-hint plotting if I have already done rgt-hint footprinting and rgt-motifanalysis matching and have the output bed files from those? I tried to run the rgt-hint plotting module with following parameters:

rgt-hint plotting --organism hg38 \
--region-file [outputFromRGTfootprinting1] \
--motif-file /path/to/rgtdata/motifs/jaspar_vertebrates/MA0007.3.Ar.pwm \
--reads-file [bam1.bam] \
--output-location ./plotting --output-prefix=TF_footprint

As indicated I used output of rgt-hint footprinting beds for region files, specifying the motif file for the specific TF as the --motif-file (Also tested with the output file from the rgt-motifanalysis matching module here) and the bam-file as the reads-file. The code run succesfully although only few seconds, but I didn't get any output. Also, as long as I could see, it only takes one input-file whereas I would like to make similar lineplots as with the rgt-hint differential with signal from all conditions plotted.

Best, -Konsta

konsta-kukkonen commented 1 year ago

Sorry, it turned out I was just affected by momentary blindness. The rgt-hint differential had printed out lineplots for everything, also my favorite TF, so everything is good.