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Deutsches Krebsforschungszentrum Genomics Proteomics Core Facility
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Update of the ChipSeq Analysis Pipeline ChiPeAn (Version 2.0)
New version of RNA-Seq quality control pipeline EvalRSeq
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New version of RNA-Seq quality control pipeline EvalRSeq

EvalRSeq is a pipeline for assessing the quality of an RNA-Seq experiment. For a description of the first version see

http://genome.dkfz-heidelberg.de/husar/index.php?id=1365&nr=252

The following new features are implemented with version 1.2:

	1. More organisms/assembly versions available
		- Human GRCh38 (GRCh37 still available)
		- Fruitfly BDGP 6
		- Cow UMD3.1

2. There is a parameter now how to deal with duplicates in the final BAM file. Duplicates can be either marked, removed, or kept.

3. Gene coverage analysis The "Coverage Information chart" lists the percentages of genes with coverage of exactly (normal) and at least (cumulative) N, with N covering all integer values of the coverage range (1 to 40 by default). At the end of the table, the percentage of genes below and above the minimum and maximum values is shown.

4. Biotype distribution There is a new chart showing the distribution of bioytpes for the genes the reads were mapped to. Genes are only counted if the number of reads mapped to it is higher than a certain threshold (default 1).

5. Biotype specific qc-metrics For all biotypes with more than a specified number of genes (default 30), a QC-Metrics analysis is performed. Number and percentage of Coding Bases, UTR bases, and intronic bases are shown.

Your HUSAR team 02/09/17