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How to incorporate personal ChIP-Seq Data Into Pyscenic?

Open rayajallad opened this issue 6 months ago • 0 comments

Hey there! I had originally used pyscenic for C. elegans data using my single cell RNA seq data. However, I want to incorporate my lab's ChIP-Seq data that hasn't been published yet. When reading the documentation I found that ChIP-Seq data was only mentioned in regards to track and BigWig files. I'm not particularly familiar with these formats. Would you perhaps have some suggestions/references on how to incorporate my lab's ChIP-Seq data into the appropriate format? I attached below the ChIP-Seq file I am working with and trying to include in my analysis. Thank you!

chr start stop name score strand signalval pval (-log10) qval (-log10) peak chr TSS_window_start TSS_window_stop GeneID  
I 0 496 MACS2_callpeaks_on_merged_peak_1 123 . 1.50088 15.22856 12.3319 282 I 0 8909 WBGene00023193
I 10034962 10035283 MACS2_callpeaks_on_merged_peak_256 34 . 1.52447 5.56146 3.40073 133 I 10025174 10035174 WBGene00008665
I 10034962 10035283 MACS2_callpeaks_on_merged_peak_256 34 . 1.52447 5.56146 3.40073 133 I 10028190 10038190 WBGene00196146
I 10034962 10035283 MACS2_callpeaks_on_merged_peak_256 34 . 1.52447 5.56146 3.40073 133 I 10029816 10039816 WBGene00003564
I 10034962 10035283 MACS2_callpeaks_on_merged_peak_256 34 . 1.52447 5.56146 3.40073 133 I 10032840 10042840 WBGene00198497
I 10034962 10035283 MACS2_callpeaks_on_merged_peak_256 34 . 1.52447 5.56146 3.40073 133 I 10035223 10045223 WBGene00196679
I 10121940 10122293 MACS2_callpeaks_on_merged_peak_257 61 . 1.67697 8.58683 6.15372 227 I 10112061 10122061 WBGene00013704
I 10121940 10122293 MACS2_callpeaks_on_merged_peak_257 61 . 1.67697 8.58683 6.15372 227 I 10112159 10122159 WBGene00013704

rayajallad avatar May 28 '25 18:05 rayajallad