Question: index genome using haploid genome.fa or diploid genome.fa?
0
gravatar for yiren
4 weeks 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 • 100 views
ADD COMMENTlink written 4 weeks 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 weeks ago by lieven.sterck6.4k

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 weeks 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 weeks ago by h.mon28k

thank you very much h.mom.

ADD REPLYlink written 4 weeks ago by yiren0

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

ADD REPLYlink written 4 weeks ago by Pierre Lindenbaum124k

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 weeks ago by yiren0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1010 users visited in the last hour