I routinely mark (I do not delete) my duplicate reads using Picard MarkDuplicate wether I do gDNA seq or RNA Seq but I still ignore (besides for GATK) which downstream software do take the marking into account and HOW.
Could someone comment on the way one should handle duplicate reads (optical & PCR types) in counting for RNASeq or variant analysis.
If you know that a particular piece of software does something by default, please let me know!
HTSeq
featureCount (has a arg --ignoreDup; who uses it?)
bcftools/samtools
varscan
Thanks for your info
Could someone comment on the way one should handle duplicate reads (optical & PCR types) in counting for RNASeq or variant analysis.
If you know that a particular piece of software does something by default, please let me know!
HTSeq
featureCount (has a arg --ignoreDup; who uses it?)
bcftools/samtools
varscan
Thanks for your info
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