Difference between revisions of "HLab:Qualitymetrics"
From CCGB
| Line 8: | Line 8: | ||
*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. | ||
| − | + | **ChIP-seq Guidelines from ENCODE (2012) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ article] | |
RNA-seq | RNA-seq | ||
Revision as of 13:20, 1 August 2014
ChIP-seq
- 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.
- ChIP-seq Guidelines from ENCODE (2012) article
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
