-1at the fourth or fifth column. For example, let's assume you have a TRE, whose coordinate is chr1:123456-123789, and it's only been observed to have transcription activity on the forward strand (TSS 123555), then the corresponding dTRE record should be:
chr1 123456 123789 . 123555 -1
bedtools intersect -a test.dtrebed -b promoters_1kb_tss_centered.bed -u > test.proximal.dtrebedTo obtain distal (also genic) TREs from the mixed dTRE file, you can use the following command:
bedtools intersect -a test.dtrebed -b promoters_1kb_tss_centered.bed -v > test.distal.dtrebed
The default annotations files downloaded from our catalog database are organized in bed-like format. Below are the columns that you will find in these annotation files:
AssayName(PubMedID), and multiple pieces of evidence will be concatenated by
MPRA(27259154)@CRISPR(31784727)); otherwise, we will put NY (Not Yet) here.
@, and if none of these signals are enriched, we put Other in this column.
pl_DPR_start-pl_DPR_end;mn_DPR_start-mn_DPR_end;pl_TATA_start-pl_TATA_end;mn_TATA_start-mn_TATA_end;pl_Inr_start-pl_Inr_end;mn_Inr_start-mn_Inr_end. If our portal cannot find any of these core promoters, the start and end coordinates will be -1.