View source for HLab:Qualitymetrics

== ChIP-seq ==
ChIP-seq Guidelines from ENCODE (2012) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ 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.
;Duplication level
: The duplication rate reported by FastQC.  It is based on all reads even those that do not map.
;Percent GC
: The percent of nucleotides that are GC as reported by FastQC.  It is based on all reads even those that do not map.
;MAD of log ratios
: mean absolute deviation of log ratios, Rafa's measure for replicate quality

== RNA-seq ==
Standards, [http://encodeproject.org/ENCODE/protocols/dataStandards/ENCODE_RNAseq_Standards_V1.0.pdf Guidelines] and Best Practices for RNA-Seq V1.0 (June 2011)
;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.
;Duplication level
: The duplication rate reported by FastQC.  It is based on all reads even those that do not map.
;Percent GC
: The percent of nucleotides that are GC as reported by FastQC.  It is based on all reads even those that do not map.
;Strand specificity
: Three numbers from RSeQC infer_experiment.py that describe the strandedness of the reads. It speculates how RNA-seq sequencing were configured, especially how reads were stranded for strand-specific RNA-seq data, through comparing reads’ mapping information to the underneath gene model. For stranded experiments the numbers are expected to approach .99:.01:0, or .01:.99:0 for unstranded .50:.50:0.
;MAD of log ratios
: mean absolute deviation of log ratios, Rafa's measure of replicate quality. Only looks at genes that are non-zero in both replicates.

Return to [[HLab:Main]]