If I am working with a large set of paired end RNA-seq samples (matched tumor, normal). In which part of the pipeline is the RG suppose to be naturally added into the header for RNA-Seq. I saw Bowtie2 has an option but I am wondering if it's common to align RNA-seq in a splice-nonaware aligner before TopHat for the sole purpose of retrieving a bam file with RG in its header.
Ideally, picard AddOrReplaceReadGroup will work but I cannot individually fetch and input the appropriate tag value for RG-ID for each paired-end samples. Thank you very much for your time and help.
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written
by
umn_bist •
1 answer
I think the optimal time to add a RG tag is either during alignment (if possible) or post-alignment before any further processing. Can you elaborate on why you cannot call picard on each aligned sample?
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written
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Patrick_Reed •
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