The choice of the bed file about cistopic

[cbravo93]

Hi @ytang0831 !

You can use any of them, if you have bulk I would use those. Another option that we have seen gives more resolution is to use a set of predefined cis-regulatory regions, such as SCREEN regions (https://screen.encodeproject.org) or cisTarget regions (available in this package for hg19, dm3, dm6 and mm9, e.g. data(hg19_CtxRegions)).

Hope this helps!

C

[ytang0831]

Thanks for your quick reply!
By the way, when I use createcisTopicObjectFromBAM funciton, region bed file is bulk data peaks, and I get a very low Successfully assigned alignments rates, e.g
||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| Read reduction : to 5' end ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required

Total alignments : 18289051 ||
|| Successfully assigned alignments : 105211 (0.6%) ||
|| Running time : 0.88 minutes

Is this normal?

[cbravo93]

mmmm not really... What is the correlation between your single cell aggregate and your bulk?

C

[ytang0831]

emmm, This should be the reason for the low correlation between single cell data and bulk data.Since I use the build-in data mm9_CtxRegions, the result improved to 7%
Thanks for help me a lot !

I'm also confused about the command path_to_signatures <- 'data/ChIP-seq_signatures/'
Which files should be signatures? Histone marker bed?(eg. use encode H3K36me3 to call peaks)? While do you have build-in data of signatures？😂

[ytang0831]

I have known the signatures meaning, a very basic question!