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Does star mark duplicates?
1. with –bamRemoveDuplicatesType UniqueIdentical, STAR does not “remove” the duplicates from the bam, but mask them as PCR duplicates by turning on a bit in the bitflag field. If you do `samtools view -c` on the input and output files, they will have exactly the same reads.
What is a duplicate read?
Read duplication may be natural (the same DNA fragment occurs and is sequenced twice) or artificial (during the sequencing procedure a copy of the same read is created and sequenced). Some approaches are more sensitive to read duplication than others.
Does RNA duplicate?
The vast majority of RNA-seq data are analyzed without duplicate removal. Thus, the occurrence of “duplicated reads” in between millions of reads can be expected even in paired-end read data. Short transcripts and very highly expressed transcripts will show the majority of such “natural” duplicates.
When to use MarkDuplicates ( Picard ) in GATK?
MarkDuplicates (Picard) GATK Team. 1 year ago. Updated. Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library construction using PCR.
How to mark all optical duplicates in Picard?
Invoking the TAGGING_POLICY option, you can instruct the program to mark all the duplicates (All), only the optical duplicates (OpticalOnly), or no duplicates (DontTag).
When do you use MarkDuplicates ( Picard ) in Bam?
MarkDuplicates (Picard) Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. Duplicates can arise during sample preparation e.g. library construction using PCR.
What causes duplicate reads in a PCR sample?
Duplicates can arise during sample preparation e.g. library construction using PCR. See also EstimateLibraryComplexity for additional notes on PCR duplication artifacts. Duplicate reads can also result from a single amplification cluster, incorrectly detected as multiple clusters by the optical sensor of the sequencing instrument.