Reference Genomes
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Human, UCSC hg19—This reference genome is PAR-masked. This means that the pseudoautosomal regions of the Y chromosome are masked to Ns to avoid mismapping of reads. |
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Human, NCBI GRCh38Decoy—This reference genome is PAR-masked. |
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Chicken, Ensembl Galgal4 |
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Pig, Ensembl Sscrofa10.2 |
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Rice, Ensembl IRGSP-1.0 |
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Sheep, Ensembl Oar_v3.1 |
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Custom Genome—Select a FASTA file (*.fa or *.fasta) as the custom genome for the analysis. |
Note
When using a custom manifest file, specify a reference genome in the [Header] section or Build ID column of the [Probes] section. The build ID, such as hg19 or GrCh38Decoy, is case-sensitive and is used to match a built-in genome. However, if you are using a custom manifest file with a custom genome, the Build ID column of the [Probes] section is not used to find the reference genome.