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Xieeeee / Droplet-Hi-C

🍹This repo includes the scripts and analysis notebook for the Droplet Hi-C manuscript
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Hello, could you please tell me where to download the research-related data mentioned in the script? #4

Open Jasonfengjx opened 2 hours ago

Jasonfengjx commented 2 hours ago

For example, in the 02.mouse_cortex_cell_types_analysis_1.ipynb script, the output directory is set to '../04.matrices/mFC_240101_DPT_rna_annotate/compartment/dchic/', but I can't find the related file.

Xieeeee commented 1 hour ago

Hi, Can you tell me which specific data or files you need? Thanks!

Best, Y

Jasonfengjx commented 1 hour ago

Hi,

We have noticed that the 02.mouse_cortex_cell_types_analysis_1.ipynb script utilizes many files, including 04.matrices/LC462_LC716_mm10.mcool::resolutions/100000 and various files within the 04.matrices/mFC_240101_DPT_rna_annotate folder. Could you please send the relevant files from the 04.matrices folder to help us run your script?

Thank you!

Xieeeee commented 1 hour ago

Hi Jiuxin, I can absolutely providing you the LC462_LC716_mm10.mcool file. All the other files especially the single cell files from these two libraries can be generated from fastq with the scripts provided in the pre-processing folder.

Since there is a huge amount of cells and we have files per cell after imputation, it would be hard for me to deposit the fully processed files, however you can find the critical files (like .pairs, where you can split single cells from it) on GEO too.

Best, Y

Jasonfengjx commented 1 hour ago

Hi, my email is 1264512262@qq.com Thanks,