This report was generated on 31/10/2022 by RASflow_EDC on iPOP-UP cluster.
The settings used for the analysis can be found in the logs/20221031T1606_configuration.txt.
The FASTQ files were not downloaded from SRA, but come from your personal data.
QC report could not be found. Have you run QC before the rest of the analysis? If not, all the results might be impaired by low quality FASTQ reads. Running QC on raw sequences is highly recommended!
Raw sequences were trimmed. A summary of the quality of the trimmed sequences can be found in
report_quality_control_after_trimming.html.
The mapping was done using HISAT2.
Mapping quality is assessed in mapping_HISAT2/report_align_count_featureCounts.html.
This report also contains an overview of feature counting that was perfomed by featureCounts.
Raw count tables are available in mapping_HISAT2/counting_featureCounts/countTables/ [Raw counts are not available in the online report].
To assess the quality of the experiment and the reproducibility of the replicates, please use the interactive MDS plot.
A static principal component analysis for all the samples is also available, as well as a heatmap with sample clustering.
You have enable the analysis of repeated elements using featureCounts.
Raw count tables for repeats are available in mapping_HISAT2/repeats_featureCounts/countTables/ [Raw counts are not available in the online report].
An interactive MDS plot based on repeat information only is shown at MDS plot.
A static principal component analysis for all the samples is also available, as well as a heatmap with sample clustering.
You have made one pairwise comparison using DESeq2. Please see below the results for this comparison.
The regionReport exploratory report is a good start to get an idea of the results.
Glimma interactive MDS plot can help you to identify problematic samples.
To be easily shared and reused the PCA and the heatmap with sample clustering are also available as PDF files.
DEA result tables (all genes or significantly differentially expressed genes) are stored in mapping_HISAT2/counting_featureCounts/DEA_DESeq2/Tables [not available in the online report].
Importantly, the results can be deeply explored thanks to interactive MD and Volcano plots.
A static Volcano plot is also available, as well as a heatmap of the 30 top-regulated genes.
The regionReport exploratory report is a good start to get an idea of the results.
Glimma interactive MDS plot can help you to identify problematic samples.
To be easily shared and reused the PCA and the heatmap with sample clustering are also available as PDF files.
DEA result tables (all repeats or significantly differentially expressed repeats) are stored in mapping_HISAT2/repeats_featureCounts/DEA_DESeq2/Tables [not available in the online report].
Importantly, the results can be deeply explored thanks to interactive MD and Volcano plots.
A static Volcano plot is also available, as well as a heatmap of the 30 top-regulated repeats.