ATAC-seq profiles at SP1 binding sites

[carushi]

Hi @HNeikes,

Thank you so much for sharing your amazing results in your BANC-seq paper! I'm strongly interested in the comparison of your results with existing ChIP-seq data, and accidentally found that one of the processed ATAC-seq data (GSE219034_R1_NPCvsESC_ATACseq_atSP1HighConfSites.txt) uploaded to GEO only contains chr1, 10, and 11 info as shown.

Since the number of lines is just same with that of "GSE193553_R1_mESC_NPC_FLAG_SP1_CUTaRUN_relEnr_Kds.txt" and total conf binding sites in Fig3d, I am concerned anything wrong happened in the file.

Sorry in advance for contacting via github since I couldn't contact with you via X or find your email address on GEO.

Thank you.
@carushi

wc -l GSE193553_R1_mESC_NPC_FLAG_SP1_CUTaRUN_relEnr_Kds.txt                                                                
    9002 GSE193553_R1_mESC_NPC_FLAG_SP1_CUTaRUN_relEnr_Kds.txt

wc -l GSE219034_R1_NPCvsESC_ATACseq_atSP1HighConfSites.txt
    9002

cut -d"   " -f1 GSE193553_R1_mESC_NPC_FLAG_SP1_CUTaRUN_relEnr_Kds.txt | sort | uniq -c                                                                                                               
   1 Chr
 475 chr1
 472 chr10
 763 chr11
 310 chr12
 294 chr13
 274 chr14
 396 chr15
 266 chr16
 434 chr17
 229 chr18
 327 chr19
 656 chr2
 381 chr3
 647 chr4
   5 chr4_GL456216_random
   2 chr4_JH584295_random
 610 chr5
 445 chr6
 730 chr7
 567 chr8
 496 chr9
   4 chrM
 216 chrX
   2 chrY

cut -d"   " -f1 GSE219034_R1_NPCvsESC_ATACseq_atSP1HighConfSites.txt | sort | uniq -c                                                                                                                
   1 Chr
4902 chr1
3595 chr10
 504 chr11