PiGx-ChIPseq - Quality control of ChIP-seq data Report
BIMSB Bioinformatics Platform
2018-07-09 21:24:18
This report was generated with PiGx ChIPseq version 0.0.20.
1 Sample Correlation
The following figure shows clustering of normalized ChIP signal, quantified in 1 kb bins. The color scale represents spearman correlation coefficient. The samples should cluster based on their biological function, and not based on batch effects or latent variables.
2 Inter Strand Cross Correlation
Inter strand cross-correlation show the correlation of ChIP signal between Watson and Crick strands. The coverage vectors are firstly shifted by the designated amount and correlation coefficient is calculated from the resulting vectors. If the DNA shearing, chromatin immunoprecipitation, and fragment selection were succesfull, the maximum value of the, per sample, distribution should correspond to the average fragment length.
3 GC Content Vs Number of Reads
The figure shows the dependence of read counts on the GC content, quantified over 1 kb bins. The plot is a diagnostic for proper fragment selection and PCR amplification.
3.1 GC Content Distribution Per Sample
The following sets of plots show, for each sample the dependence of read counts on the GC content.
3.1.1 mm_wt_d1_h3k27ac_br1
3.1.2 mm_wt_d1_h3k27ac_br2
3.1.3 mm_wt_d1_h3k27me3_br1
3.1.4 mm_wt_d1_h3k27me3_br2
3.1.5 mm_wt_d1_h3k36me3_br1
3.1.6 mm_wt_d1_h3k36me3_br2
3.1.7 mm_wt_d1_h3k4me1_br1
3.1.8 mm_wt_d1_h3k4me1_br2
