I am trying to a recently published software called diffTF and contacted the authors on how to obtain the input HOCOMOCO files for GRCh38. While I wait for the answer, I thought I would post the question here as well:
The tool requires bed files for each of the transcription factors (TF) in the genome, such as this bed file (TAB separated), which seems to give the locations of different TF binding sites in the genome:
chr1 3457132 3457141 GTTGCGTGA 1266 + chr1 4595374 4595383 GTTGCGTGA 1266 - chr1 4996631 4996640 TTTGCGTGC 1276 + chr1 5005357 5005366 TTTGCGTGC 1276 + chr1 5170456 5170465 TTTGCGTGC 1276 - chr1 5567302 5567311 GTTGCGTGA 1266 - chr1 8676279 8676288 TTTGCGTGC 1276 - chr1 8859719 8859728 GTTGCGTGA 1266 + chr1 9600920 9600929 GTTGCGTGA 1266 + chr1 9650971 9650980 GTTGCGTGA 1266 + ...
Then there is a symbols file to map the TF to their gene(?) that looks like this:
SYMBOL ENSEMBL HOCOID Ahr ENSMUSG00000019256 AHR Aire ENSMUSG00000000731 AIRE Alx1 ENSMUSG00000036602 ALX1 Ar ENSMUSG00000046532 ANDR Tfap2a ENSMUSG00000021359 AP2A Tfap2b ENSMUSG00000025927 AP2B Tfap2c ENSMUSG00000028640 AP2C Tfap2d ENSMUSG00000042596 AP2D
I googled for HOCOMOCO and found a bunch of pwn or words files, but none of them seems to be similar to the bed file above. Any ideas where to get these for GRCh38?