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aanderson54 / Loupe_BrainTF

All code generated for Loupe et al. 2023
MIT License
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File name meaning #2

Closed zhangpicb closed 2 weeks ago

zhangpicb commented 2 weeks ago

Hi @aanderson54 @jloupe

Thanks for the great resource! Brain TF bed file downloaded from https://www.synapse.org/Synapse:syn51942384.5/datasets/ DLPFC tissue TF ASH2L have 4 files,DLPFC-NEG mean not neuron cells? what's the difference between Output_idr.optimal_peak.regionPeak.gz and Output_ppr.IDR0.05.filt.narrowPeak.gz?

ASH2L_DLPFC-NEG_Output_idr.optimal_peak.regionPeak.gz ASH2L_DLPFC-NEUN_Output_idr.optimal_peak.regionPeak.gz ASH2L_DLPFC-OLIG_Output_idr.optimal_peak.regionPeak.gz ASH2L_DLPFC_Output_ppr.IDR0.05.filt.narrowPeak.gz

Thanks in advanced!

aanderson54 commented 2 weeks ago

The first three files listed are from sorted DLPFC tissue. NEUN is NeuN+ (neurons), OLIG is Olig2+ (oligodendrocytes), and NEG is NeuN- and Olig2- (mostly astrocytes/microglia). The last file is from bulk tissue.

The regionPeak and narrowPeak file types are equivalent. The naming strategy changed in the updated version of the ENCODE ChIP-seq pipeline, but the peaks are called using the same method.

Please let me know if you have any other questions!

Ashlyn

zhangpicb commented 2 weeks ago

Thanks again!