Hello,
I have RNA-seq data sequenced in Illumina platform.
I have run the quality control with FASTQC and indeed, I have detected duplicates. As I am going to use these sequence data to do the SNP calling, I must remove the duplicates.
Does anyone have any experience with this? what is the best way to remove the duplicates, before mapping or when I start with the SNP calling with gatk?
Also, what are the software suggested for this purpose.
Thanks a lot in advance.
PS: I have posted this question to www.biostars.org/p/66831/, the answers are not consensus.
I have RNA-seq data sequenced in Illumina platform.
I have run the quality control with FASTQC and indeed, I have detected duplicates. As I am going to use these sequence data to do the SNP calling, I must remove the duplicates.
Does anyone have any experience with this? what is the best way to remove the duplicates, before mapping or when I start with the SNP calling with gatk?
Also, what are the software suggested for this purpose.
Thanks a lot in advance.
PS: I have posted this question to www.biostars.org/p/66831/, the answers are not consensus.
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