HLab:Qualitymetrics

ChIP-seq

ChIP-seq Guidelines from ENCODE (2012) article

• FRIP

  Fraction of Reads in Peaks, a value of greater than or equal to 0.01 is considered good.

• NSC

  Normalized Strand Coefficient, The normalized ratio between the fragment-length cross-correlation peak and the background cross-correlation.  A value of greater than or equal to 1.05 is considered good.

• RSC

  Relative Strand Correlation, ratio between the fragment-length peak and the read-length peak. A value of greater than or equal to 0.8 is considered good.

• Complexity

  This is computed on a sampling of the reads if more than 10M, using Georgi's method. A value greater than or equal to 0.80 is considered good.

RNA-seq

• FRIT

  Fraction of Reads in Target, for Total script this is anywhere in the gene.  

• Percent rRNA

  Percent of the alignments that overlap rRNA as downloaded from UCSC.

• Number of expressed genes

  Count of genes with RSEM TPM greater than 1.  Should be similar between replicates.

• Number of spike-ins

  Count of reads mapping to spike-ins.