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2 hours ago by

I wish to align my mouse WES fastq files using a GRCM38 reference genome. I found the genome in the USNC portal (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?



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