Parser and tools for summarising outputs of samtools stats, with ATAC-seq in mind. It's greatest feature will be the possiblility to fit the distribution of exponential and gaussians into IS distribution (never happend still usefull for parsing samtools stats output :). And it will present all this with userfriendly shiny interface.
Standards from encodeproject
- two or more biological replicates
- at least 25 million fragments
- aligment rate greater than 95%
- replicate concordance measuredby calculating IDR values
- library complexity measured using Non-Redundant Fraction and PCR Bottlenecking Coefficients 1 and 2. NRF > 0.9, PBC1 > 0.9, PBC2 > 3
- mononucleosome peak must be present in the fragment length distribution
- FRiP > 0.3
- TSS enrichment