Pervasive transcription in the human genome exceeds background noise

Repository contains:Experimental GRO-capLift_T2T_Masks_to_GRCh38chm13v2-hg38.over.chain.gz - chain file used for mask liftover (T2T to GRCh38)Lift_to_T2Tchr_to_nc.tsv - UCSC to NCBI format conversion tablehg38-chm13v2.over.chain.gz - chain file used for liftover (GRCh38 to T2T)unmapped.txt - regions that failed liftoverenbw_plus_HPRT1.bedgraph - Experimental GRO-cap data of HPRT1 region onlyenbw_plus_perbp.bedgraph - Experimental GRO-cap data, one nucleotide per rowFastasHoldout_and_HPRT1chr8:89,892,879-89,992,878.fasta - 100 kb region within Puffin-D holdout chromosomes used in supplementary figures plotting Puffin-D outputHPRT1_100kb.fasta / HPRT1R_100kb.fasta / HPRT1rNoCpG_padded.fasta - 100 kb HPRT1 variations used in Camellato et al., 2024.T2T_fastas_by_chr - By-chromosome fasta files containing 100 kb chunks for the T2T forward genome.Puffin-D Numpy ArraysHoldout_and_HPRT1 - Puffin-D Numpy outputs for 100 kb Holdout region and HPRT1 variants.chr8_89,892,879-89,992,878.npyHPRT1.npy / HPRT1R.npy / HPRT1RnoCpG_AllRightPad.npy - 100 kb HPRT1 variations used in Camellato et al., 2024.Transposon_Analysesdatasets_positions.tsv - list of datasets and corresponding GRO-cap TSS position .bed files (for use with summarise_repeat_nonrepeat.rscript)each .bed file listed in datasets_positions.tsv (including 'GROcap_chm13_nc_perbp.bed' - Experimental GRO-cap data lifted to the T2T genome)Inter-cluster distance distribution across read thresholds movie.gif - GIF showing the changing distribution of inter-cluster distances across varying read thresholds.