In Silico Fast.gz files for UMI data? (Unique Molecular Identifiers)

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2.5 years ago

Michael ▴ 10

I need to create in silico reads for umi data. Is there any software out there? I need to create a non-consensus and consensus bam with known inputs to validate a pipeline.

fastq in-silico umi • 899 views

ADD COMMENT • link 2.5 years ago by Michael ▴ 10

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I just found this: https://gitlab.com/vincent-sater/umigen . UMI's add a level of complexity and cost to the experimental procedures. They are probably not widely used routinely outside of single-cell technologies like 10x.

What kind of data are you looking to simulate (WGS, WES, RNAseq)? What is the non-consensus/consensus referring to?

ADD REPLY • link 2.5 years ago by GenoMax 154k

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Somatic variants, rna-seq, WES, all sorts of stuff.

We use fgbio CallMolecularConsensus to call the consensus reads.

ADD REPLY • link 2.5 years ago by Michael ▴ 10

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