Entering edit mode
3.3 years ago
Apprentice
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160
Hi.
I would like to use GRCh38 as a reference sequence for NGS data analysis. I tried to get the file of GRCh38 at iGenomes. https://jp.support.illumina.com/sequencing/sequencing_software/igenome.html
At the site, I noticed that there is the link of decoy for only GRCh38 (GRCh38decoy). It seems that there is no link of decoy for hg38, hg19, GRCh37. Why is there the link for only GRCh38?
When I use the GRCh38 as a reference sequence for NGS data analysis, should I use GRCh38decoy? If I should use it, could you please tell me how to use it?
Please see A: Decoy In Reference Assembly
Thank you for your quick reply. I know some general things about a decoy in reference assembly. I would like to know why there is the link of decoy for only GRCh38 at the iGenomes and how I should use the decoy in this case.
As an aside, iGenomes is not maintained and I believe the last update was in 2015. You may want to look into other options for maintaining your genomes and annotations. refgenie is an attractive alternative.
Thank you for your advice. I understand the iGenomes is not maintained. I will look into other options.
You simply include the decoy as an extra chromosome into the reference genome, so it "captures" the problematic alignments. Beyond that there is not much to do with it. It is simply a sequence to capture problematic reads which would aberrantly align to the main chromosomes and give false variant calls. I am not sure why it is not in 37, maybe because it is super-old and they did not bother? I guess using the decoy makes sense when you are interested in variant calling, not sure if there is a benefit for other applications like, say, ChIP-seq.
Thank you for your advice.