Interface definition: WP6 <- WP1/2

[oKoch]

Usecase 1:

1. Finding transcription factor binding sites with tf_comb
2. Market basket analyses for finding transcription factor binding sites

Files should be delivered by WP1 and WP2 ! Required files and conventions:

• We need the ../path to your result folder.
• Please name the file with the selected celltype or cell cluster: e.g. <_cell_type_or cell_cluster_name_>.bed
• file structure: chromosome ; open-chromatin-region (100503870 - 100506200) ; Annotation/tag .bed: ``` chr1 100503870 100506200 RP4-714D9.5,HIAT1 chr1 100713300 100715320 HIAT1,BRI3P1,DBT,RTCD1 chr1 100818560 100819310 BRI3P1,RP5-837M10.1,CDC14A,BCAS2P2 ``` Example file: [A375_enhancers.bed.zip](https://github.com/loosolab/Datenanalyse-2021/files/7663595/A375_enhancers.bed.zip)

[oKoch]

Protocol Meeting WP2/6, 05.01.2021:

• After peak calling, wp6 needs the open-chromatin regions per celltype/cluster (file name), see (pseudo bulk merged peak)
• wp2 creates a example for one tissue after they ran through step 11 in Link (https://github.com/r3fang/SnapATAC/blob/master/examples/10X_brain_5k/README.md#peak_call)

[AGuthmann]

Protocol Meeting WP1/6, 08.01.2022:

WP1 should provide:

• Peak calling .bed-files {tissue-type}_{cluster/cell-type}.bed
• Path to output folder containing .bed-files

[Mfkessler]

Here you can find one example of WP2's peak calling: /mnt/workspace_stud/stud4/WP6_data The folder contains peak calling .bed files of every cluster from the right lobe of liver tissue.