extracting consensus from pooled sequenced samples

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9.1 years ago

meekadi ▴ 10

Dear all. I have pooled sequenced data which I need to separate. DNA from four animals was mixed together without attaching adapters and sent for sequencing. The data contains information on four samples and I need to generate a consensus for each one of the samples. I also have genotyped data for each of the samples. My question is, is there a way in which I can use the genotype (Bead chip) data as a reference to extract sequences matching each sample? Are there known programs or do I need a script for that?

ChIP-Seq Assembly next-gen-sequencing • 1.8k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 9.1 years ago by meekadi ▴ 10

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If the individual samples were not tagged/barcoded (you don't say if they were) how can you hope to cleanly separate the data into individual samples (I am assuming these samples are related and not from different taxa).

ADD REPLY • link 9.1 years ago by GenoMax 147k

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Yes, the individuals were not tagged or barcoded. I was hoping there was a method in which I could be able to use their genotyping data to separate them.

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 9.1 years ago by meekadi ▴ 10

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You may be able to separate the reads that contains a specific SNP but that does not help much since you already had that information. Sounds like you are going to need to repeat this sequencing again using barcodes.