My travails started when I tried to produce mapping stats (exons, introns, intergenic regions) for RNA-Seq samples aligned with Tophat2 and Ensembl GTF files. For a number of reasons RNA-SeQC seems to be the most appropriate tool but I am struggling to use it as I could not find a description of all the steps that I need to perform to prepare my data to be used with RNA-SeQC.
The various internet sources seem to agree that the first thing I need to do is to use AddOrReplaceReadGroups.jar with the BAM file but I could not find documentation regarding the parameters. Google finds several command line examples and they all use different parameters. My samples are single-end and are produced on Illumina MiSeq using TruSeq. This is all I know right now. What parameters shall I use with AddOrReplaceReadGroups.jar?
The various internet sources seem to agree that the first thing I need to do is to use AddOrReplaceReadGroups.jar with the BAM file but I could not find documentation regarding the parameters. Google finds several command line examples and they all use different parameters. My samples are single-end and are produced on Illumina MiSeq using TruSeq. This is all I know right now. What parameters shall I use with AddOrReplaceReadGroups.jar?
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