Question: index genome using haploid genome.fa or diploid genome.fa?
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Unless specifically done so, even diploid genomes are usually assembled in a haploid state. What species are we talking about here and do you have any insights in how it was assembled?
The species is candida albicans,like a yeast.I find the genome that is haploid state from NCBI.But in its web,they offer the diploid state genome.fa.
See these previous discussions:
C Albicans Genome Count Matrix Total Genes
Generate a counts matrix with paired-end non-stranded samples
Candida albicans gene counts
thank you very much h.mom.
which software are you using ? what is a "diploid genome fa" ?
diploid genome.fa file is that there are two chr1 such as chr1_A,chr1_B.But chr1_A,chr1_B are a pair of chromosome.