Difference between revisions of "HLab:Qualitymetrics"
From CCGB
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| − | ChIP-seq | + | == ChIP-seq == |
| + | ChIP-seq Guidelines from ENCODE (2012) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ article] | ||
| + | |||
*FRIP | *FRIP | ||
Fraction of Reads in Peaks, a value of greater than or equal to 0.01 is considered good. | Fraction of Reads in Peaks, a value of greater than or equal to 0.01 is considered good. | ||
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*Complexity | *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. | 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 | + | == RNA-seq == |
| + | |||
*FRIT | *FRIT | ||
Fraction of Reads in Target, for Total script this is anywhere in the gene. | Fraction of Reads in Target, for Total script this is anywhere in the gene. | ||
Revision as of 13:22, 1 August 2014
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
- Number of spike-ins
