<![CDATA[BOL: Carefully opt for human reference genome]]> https://bioinformaticsonline.com/bookmarks/view/41158/carefully-opt-for-human-reference-genome? https://bioinformaticsonline.com/bookmarks/view/41158/carefully-opt-for-human-reference-genome Tue, 18 Feb 2020 07:43:32 -0600 https://bioinformaticsonline.com/bookmarks/view/41158/carefully-opt-for-human-reference-genome <![CDATA[Carefully opt for human reference genome]]> Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

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