RNA-SeQC on Helix
RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
Example files are under /usr/local/apps/rnaseqc/example
Other useful data is under /usr/local/apps/rnaseqc/data
User needs to add bwa (or samtools) to the PATH by running 'module load bwa' and/or 'module load samtools'.
The following example assume that user has already copied the example directory to /home/$USER/example
How To Use
$ module load bwa $ cd /home/$USER/example $ java -jar /usr/local/apps/rnaseqc/current/RNASeQC.jar \ -n 1000 \ -s "TestId|ThousandReads.bam|TestDesc" \ -t gencode.v7.annotation_goodContig.gtf \ -r Homo_sapiens_assembly19.fasta \ -o ./testReport/ \ -strat gc \ -gc gencode.v7.gc.txt \ -BWArRNA human_all_rRNA.fasta