Picard MarkDuplicates tool on a pooled sample BAM
Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file? (Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced) Or is it meant only for a single diploid sample?
Thank you.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Duplication rate as reported by fastp.
written by Anjan
-
Can MarkDuplicates of Picard be used for RNA reads?
written by Nemo •
-
How treat a Bam file with mutiple read groups (RG)
written by zamani_2012 •
-
Feedback requested for pooling biological samples for NGS
written by kumars.sv •
-
using bash variable in picard MarkDuplicates command
written by bioguy24
-
Trouble preparing paired-end (MiSeq 2x250), double-tagged and dual-indexed reads from metabarcoding…
written by jack1120 •
-
Questions about LB field in SAM specification for PCR duplicate removal
written by James Ashmore
-
Genome coverage with pool of individuals
written by jomaco
-
samtools mpileup on pooled samples
written by koen.vdberge •
-
Differential methylation analysis: sequencing biological replicates versus pooled samples?
written by Ian
"pooled" samples and "diploid" samples are not mutually exclusive or even comparable concepts. "Diploid" refers to the number of sets of chromosomes in the organism, whereas "pooled" samples is a concept from experiment design during sequencing or downstream analysis.
Sorry, my mistake. I meant to ask: Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file?(Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced). Or is it meant only for a single diploid sample?
It does not matter how the library was made. The tool will remove sequences with identical mapping positions. There is no way to distinguish true PCR replicates from identical fragments that come from different samples prior to pooling. Typically duplicates are marked prior to any downstream application in DNA-seq.