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

0

Entering edit mode

2.7 years ago

yiren ▴ 10

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 • 872 views

ADD COMMENT • link updated 2.7 years ago by Biostar 20 • written 2.7 years ago by yiren ▴ 10

1

Entering edit mode

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 REPLY • link 2.7 years ago by lieven.sterck 14k

0

Entering edit mode

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 REPLY • link 2.7 years ago by yiren ▴ 10

0

Entering edit mode

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 REPLY • link 2.7 years ago by h.mon 34k

0

Entering edit mode

thank you very much h.mom.

ADD REPLY • link 2.7 years ago by yiren ▴ 10

0

Entering edit mode

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

ADD REPLY • link 2.7 years ago by Pierre Lindenbaum 147k

0

Entering edit mode

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 REPLY • link 2.7 years ago by yiren ▴ 10

Login before adding your answer.