msbentsen
commented
1 year ago Hi Rajashee,
total_tfbsrefers to the total number of transcription factor binding sites in the input regions given to BINDetect. These correspond to the length of the individual<TF>/beds/<TF>_all.bed-files.- The
_changecolumn is an effect-score between the raw differential footprint scores of the TF and the background sampled scores. Basically this shows whether there is an enrichment of TF-scores in condition 1 vs. 2 in comparison to background (similar to a log2fc) - there is a little bit more information to be found in the supplementary material of the TOBIAS paper here: https://www.nature.com/articles/s41467-020-18035-1#Sec22
You can also find information on the output formats on the wiki-page here: https://github.com/loosolab/TOBIAS/wiki/BINDetect
Could you please let me know where/how is the 'total_tfbs' column count derived from in the Bindetect results .xls files?
Secondly, could you also tell me how are the values in the '_change' column derived/calculated?
Thanks, Rajashree