Removing Duplicate Reads Post Alignment
Hi,
I'm analyzing RNA-Seq data and I want to check for snp in it. For that, I want to remove duplicated reads from the bam file. Duplicate reads are reads that are aligned at the same position on the genome. Could anyone help me with that ?
Thanks,
N.
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Nicolas Rosewick
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please read Removing duplicates from RNA-seq data
furthermore, please search "Removing duplicates from RNA-seq data", and please avoid duplicate posting
This has been answered several times on the site. Briefly, two options for software are samtools and picard. As far as I know, If you have paired-end data, picard is preferred. You should have a think about whether it's appropriate to remove duplicates in your situation. See link provided by Nandini.
Closing this question as a duplicate.