Question: (Closed) Removing Duplicate Reads Post Alignment
gravatar for Nicolas Rosewick
5.9 years ago by
Belgium, Brussels
Nicolas Rosewick7.5k wrote:


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 ?



reads duplicates • 2.7k views
ADD COMMENTlink written 5.9 years ago by Nicolas Rosewick7.5k

please read Removing duplicates from RNA-seq data

ADD REPLYlink written 5.9 years ago by Nandini780

furthermore, please search "Removing duplicates from RNA-seq data", and please avoid duplicate posting

ADD REPLYlink written 5.9 years ago by Jorge Amigo11k

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.

ADD REPLYlink written 5.9 years ago by KCC3.9k

Closing this question as a duplicate.

ADD REPLYlink written 5.9 years ago by Neilfws48k
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