This directory contains BED files of merged Transcription Start Sites (TSSs) generated within the GENCODE Capture Long-Seq project using PacBio HCGM reads.

These were produced by merging "*TSSs.bed" files listed in ../raw/ using the following command:

$ cat $RAW_BEDfile | bedtools merge -s -n -d 5 -nms -i stdin > <species>All_Cap1_<tissue>_TSSs.clusters.bed


All files correspond to genome assemblies hg38 and mm10.


# File naming scheme:

<species>All_Cap1_<tissue>_TSSs.clusters.bed

where:
	species:
		"mm": mouse
		"hs": human

	tissue: self-explanatory, except:
		"all": all TSSs merged across all tissues.


# BED file format (BED6):

There is one read per BED record.

    column 1: chromosome 
    column 2: chromosome start of merged TSS
    column 3: chromosome end of merged TSS
    column 4: comma-separated list of read identifiers contributing to the TSS
    column 5: number of reads contributing to the TSS
    column 6: genomic strand of the TSS