Difference between revisions of "HLab:Qualitymetrics"
From CCGB
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== RNA-seq == | == 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 | *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 14:29, 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
Standards, 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.
