How to incorporate other motif databases aside from JASPAR in STREAM analysis of scATAC dataset

[sylestiel]

Hi,

How can I incorporate homer pwms motif list and mouse pwms v2 list into the STREAM_scATAC-seq-motif.ipynb?

Thanks! SH

[huidongchen]

What do you mean by 'incorporating'? How are you planning to use them?

[sylestiel]

I want the program to be able to scan for motifs that are not present in the JASPAR database. I think the motif ipynb only scans 128. I want to increase the repertoire. Hence have it scan other motif databases.

SH

[huidongchen]

Thanks for clarifying the problem! The short answer is that in STREAM we are not supporting other motif databases except for JASPAR2016 yet.

But that's something definitely on our to-do-list. In STREAM we are internally calling chromVAR (an R package) to scan and score motifs. We still need to further check and test the compatibility of these databases with our python dependencies before adding them. But hopefully we will include more motif collections very soon. Stay tuned!

[sylestiel]

Okay. Thanks!

On June 29, 2020 at 10:07 AM Huidong Chen [email protected] wrote:

Thanks for clarifying the problem! The short answer is that in STREAM we are not supporting other motif databases except for JASPAR yet.

But that's something definitely on our to-do-list. In STREAM we are internally calling chromVAR (an R package) to scan and score motifs. We still need to further check and test the compatibility of these databases with our python dependencies before adding them. But hopefully we will include more motif collections very soon. Stay tuned!

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