<b>Most pervasive transcription in </b><b>the human</b><b> genome is </b><b>inconsistent with background noise</b>

<p dir="ltr">Repository contains:</p><ul><li>Experimental_Grocap</li><li><ul><li>Lift_T2T_Masks_to_GRCh38</li><li><ul><li>chm13v2-hg38.over.chain.gz - chain file used for mask liftover (T2T to GRCh38)</li></ul></li><li>lift_to_T2T</li><li><ul><li>chr_to_nc.tsv - UCSC to NCBI format conversion table</li><li>GROcap_chm13_nc_sorted.bed - Experimental GROcap data lifted to T2T genome</li><li>hg38-chm13v2.over.chain.gz - chain file used for liftover (GRCh38 to T2T)</li><li>unmapped.txt - regions that failed liftover</li></ul></li><li>enbw_plus_HPRT1.bedgraph - Experimental GROcap data of HPRT1 region only</li><li>enbw_plus_perbp.bedgraph - Experimental GROcap data, one nucleotide per row</li></ul></li><li>Fastas</li><li><ul><li>Holdout</li><li><ul><li>chr8:89,892,879-89,992,878.fasta - Selected 100kb region within Puffin-D holdout chromosomes used in supplementary figures plotting Puffin-D output</li></ul></li><li>HPRT1</li><li><ul><li>HPRT1_100kb.fasta / HPRT1R_100kb.fasta / HPRT1rNoCpG_padded.fasta - HPRT1 variations used in Camellato et al., 2024.</li></ul></li><li>T2T_fastas_by_chr - By-chromosome fasta files containing 100kb chunks for the T2T forward and reverse genomes.</li></ul></li><li>Puffin-D Numpy Arrays</li><li><ul><li>Holdout / HPRT1 - Puffin-D Numpy outputs for Holdout region and HPRT1 variants.</li></ul></li><li>Inter-cluster distance distribution across read thresholds movie.gif - Gif showing the changing distribution of inter-cluster distances across varying read thresholds.</li><li>datasets_positions.tsv - list of datasets and corresponding GROcap TSS positions bed files (for use with summarise_repeat_nonrepeat.rscript)</li></ul><p><br></p>