index genome using haploid genome.fa or diploid genome.fa?

Question

[yiren]

hi,now,I have a question about index genome in RNAseq.My species is diploid,but my genome file fasta is diploid,how can I index my genome?Can I delete my genome to haploid for index?

[lieven.sterck]

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?

[yiren]

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.

[h.mon]

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

[yiren]

thank you very much h.mom.

[Pierre Lindenbaum]

which software are you using ? what is a "diploid genome fa" ?

[yiren]

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.