rna seq – Which candida albicans fasta and gff file should I use for alignment?

The refseq is Candida albicans SC5314.

I assume you are performing a fasta reference based assembly.

Its 8 chromosomes are NC_032089.1 to NC_032096.1 inclusively from chromosome 1 to chromosome 7 (NC_032095.1) to chromosome R.

Its here.

Most of the files you downloaded are SC5314. So I dunno it depends what the project is re-annotation, reassembly?

The vcf is a very interesting file, particularly if you are sequencing your own variants of Candida.

Whats in all the files:

  • C_albicans_SC5314_A22_current_orf_coding.fasta.gz proteins ignoring introns – useful
  • C_albicans_SC5314_A22_current_chromosomes.fasta.gz is going to be NCBI files I described.
  • C_albicans_SC5314_A22_current_default_protein.fasta.gz orfs splicing out the introns

… list goes on really it depends on the project. I would recommend current only. A22-s07-m01-r179 will likely be the previous assembly / annotation.

I guess the single file you want is C_albicans_SC5314_A22_current_chromosomes.fasta.gz for referenced based assemblies (presumably of Candida isolates).

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