print tables reporting encode quality control metrics

[alexg9010]

https://www.encodeproject.org/atac-seq/

• Experiments should have two or more biological replicates. Assays performed using EN-TEx samples may be exempted due to limited availability of experimental material, but at least two technical replicates are required.
• Each replicate should have 25 million non-duplicate, non-mitochondrial aligned reads for single-end sequencing and 50 million for paired-ended sequencing (i.e. 25 million fragments, regardless of sequencing run type).
• The alignment rate, or percentage of mapped reads, should be greater than 95%, though values >80% may be acceptable.
• Replicate concordance is measured by calculating IDR values (Irreproducible Discovery Rate). The experiment passes if both rescue and self consistency ratios are less than 2.
• Library complexity is measured using the Non-Redundant Fraction (NRF) and PCR Bottlenecking Coefficients 1 and 2, or PBC1 and PBC2. The preferred values are as follows: NRF>0.9, PBC1>0.9, and PBC2>3.
• Various peak files must meet certain requirements. Please visit the section on output files under the pipeline overview for more information on peak files.
  • The number of peaks within a replicated peak file should be >150,000, though values >100,000 may be acceptable.
  • The number of peaks within an IDR peak file should be >70,000, though values >50,000 may be acceptable.
  • A nucleosome free region (NFR) must be present.
  • A mononucleosome peak must be present in the fragment length distribution. These are reads that span a single nucleosome, so they are longer than 147 bp but shorter than 147*2 bp. Good ATAC-seq datasets have reads that span nucleosomes (which allows for calling nucleosome positions in addition to open regions of chromatin).
• The fraction of reads in called peak regions (FRiP score) should be >0.3, though values greater than 0.2 are acceptable. For EN-TEx tissues, FRiP scores will not be enforced as QC metric. TSS enrichment remains in place as a key signal to noise measure.
• Transcription start site (TSS) enrichment values are dependent on the reference files used; cutoff values for high quality data are listed in the table below.