Difference between revisions of "HLab:Qualitymetrics"
From CCGB
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ChIP-seq Guidelines from ENCODE (2012) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ article] | 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. | |
== 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) | 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. | |
Revision as of 15:05, 25 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.
