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Reference mouse genome

I wish to align my mouse WES fastq files using a GRCM38 reference genome. I found the genome in the USNC portal (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/snp142Mask/). However, the fasta files are available for individual chromosomes as far as I understand. How/where to get the WES fasta file for mus musculus? Also, once aligned, I wish to annotate the variants using snpEff. But the GRCm38 genome in their database is a different version (CRCm38.75). Will this cause 'ERROR_CHROMOSOME_NOT_FOUND' error?

alignment fasta reference genome
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updated by GenoMax GenoMax • written by atheeth14 • atheeth14

This is not a forum post, but a question.

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written by Carambakaracho Carambakaracho

How/where to get the WES fasta file for mus musculus?

By using sra-explorer (search for WES mouse) . Assuming by WES you are referring to whole exome sequence. You are not going to get a fasta file. You will need to get the original fastq reads and do the analysis yourself.

NCBI Datasets is the new experimental location to get large datasets like genomes.

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written by GenoMax GenoMax

1 answer

  1. go to https://www.ncbi.nlm.nih.gov/
  2. Select genome (or assembly) and search for Mus Musculus
  3. Select genome and assembly report
  4. select the assembly of your choice, for example GRCm38 and download the assembly

As far as I know, the primary assembly is not modified with the patches, and certainly not the chromosomes added or removed

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written by Carambakaracho Carambakaracho

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