Question: index genome using haploid genome.fa or diploid genome.fa?
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gravatar for yiren
4 months ago by
yiren0
yiren0 wrote:

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?

rna-seq • 204 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by yiren0
1

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?

ADD REPLYlink written 4 months ago by lieven.sterck7.3k

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.

ADD REPLYlink written 4 months ago by yiren0

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

ADD REPLYlink written 4 months ago by h.mon29k

thank you very much h.mom.

ADD REPLYlink written 4 months ago by yiren0

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

ADD REPLYlink written 4 months ago by Pierre Lindenbaum127k

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.

ADD REPLYlink written 4 months ago by yiren0
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