Chip-seq files for topic annotation & UCSC-style bams not working about cistopic

[arutik]

Sorry, the second issue seems to be caused by the way I make my bams UCSC-like, so ignore it please.

[cbravo93]

Hi @arutik!

Regards the first point, that would depend on which system you are working on (organism/tissue/cell type). Together with ChIP-seq, other assays such as bulk ATAC-seq or DNAse (of e.g. FACS sorted cell types of your population, see the 10X tutorials) can be useful.

Apart for searching in literature/GEO, there are some ChIP-seq/bulk ATAC/DNAse/H2K27ac/... databases that you could use, such as http://cistrome.org/db/#/ (for mouse and human only), https://chip-atlas.org or https://www.encodeproject.org.

Hope this is useful!

C

[arutik]

Thank you so much!

Re issue 2 for other sufferers: make the regions file (pseudo bulk) UCSC-style and the rest of the functions will work.