Analysis tools to compare two similar Illumina targeted sequencing runs?

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10.4 years ago

14134125465346445 ★ 3.6k

What are the commonly used analysis tools to compare two similar targeted sequencing runs done with Illumina?

The type of analysis I am thinking could be useful right now are:

Amplification biases
Basecalling biases
Alignment biases
Small variant calling biases
SV calling biases
Fusion detection biases

By targeted sequencing I mean either amplicon sequencing or pull-down enrichment sequencing protocols, which is the same to say not whole genome sequencing or whole metagenome sequencing runs.

bam analysis targeted • 2.5k views

ADD COMMENT • link updated 3.9 years ago by Ram 44k • written 10.4 years ago by 14134125465346445 ★ 3.6k

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I don't think that just two runs would be sufficient to establish any of that.

ADD REPLY • link updated 3.9 years ago by Ram 44k • written 10.4 years ago by Istvan Albert 102k

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Presumably you want to look for variants rather than something else. If not, please specify the type of analysis you have in mind.

ADD REPLY • link updated 3.9 years ago by Ram 44k • written 10.4 years ago by Devon Ryan 105k

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Actually I was looking for an answer to this same question, specifically to compare coverage of amplicons between two runs, but the other points listed above would also be useful.

I prepared libraries for 8 samples with two methods of normalization for the same assay. So the amplicons and samples are the same, but we expect the coverage to possibly be different between each set. Is there a tool to compare this? It seems like people took the above question to mean to look for biological differences instead of just a technical comparison.