Add and refactor EOLs QC script

[henrikstranneheim]

• [x] Rseqc
• [x] multiqc
• [x] Preseq

Will skip:

• FeatureCounts
• dupRadar
• MIP/qccollect

[henrikstranneheim]

Script: /mnt/hds/proj/bioinfo/RNAseq/scripts/extract_QC_data.sh

[henrikstranneheim]

I think we could use these tools instead of the current EOL script.

• FeatureCounts: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. http://bioinf.wehi.edu.au/featureCounts/
• Rseqc: RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. http://rseqc.sourceforge.net/
• dupRadar: Assessment of duplication rates in RNA-Seq datasets. https://www.bioconductor.org/packages/release/bioc/html/dupRadar.html
• Preseq: preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. http://smithlabresearch.org/software/preseq/
• multiqc for aggregate statistics
• MIP/qccollect for automated FAIL/WARN/PASS key qc_metrics on the fly

[henrikstranneheim]

@jemten Done?

[jemten]

Done