how duplicates are handled?

[Richard Corbett]

Hi there,

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I’m new to ROSE and I am wondering how duplicate reads are handled in the analysis? If I was trying to see if it would help by marking duplicate different ways, should I just change the duplicate status in the BAM file?

thanks

Richard

[Richard Corbett]

I looked through the code and didn’t see anything suggesting that the duplicate status of reads in considered. For example, I don’t see anything duplicate related in getRawReads but I could be mistaken.