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I downloaded the gff and fasta files for candida albicans from http://www.candidagenome.org. I want to use hisat2 to align some fastq files against it.

There are many files in each download :

gff :

A22_ForcheSNPs.gff
A22_Historic_Assemblies.gff
A22_Jones_PMID_15123810_Polymorphisms.gff
A22_Jones_PMID_15123810_Polymorphisms.vcf
A22_Unannotated_transcripts_Bruno_et_al.gff
A22_Unannotated_transcripts_Sellam_et_al.gff
A22_Unannotated_transcripts_Tuch_et_al.gff
C_albicans_SC5314_A22_current_features.gff
C_albicans_SC5314_A22_current_features.gtf
C_albicans_SC5314_A22_current_features_with_chromosome_sequences.gff.gz
C_albicans_SC5314_A22_current_intergenic.gff
C_albicans_SC5314_haplotype_variations.gff
C_albicans_SC5314_version_A22-s07-m01-r179_features.gff
C_albicans_SC5314_version_A22-s07-m01-r179_features.gtf
C_albicans_SC5314_version_A22-s07-m01-r179_features_with_chromosome_sequences.gff.gz
C_albicans_SC5314_version_A22-s07-m01-r179_intergenic.gff

fasta :

C_albicans_SC5314_A22_current_chromosomes.fasta.gz
C_albicans_SC5314_A22_current_default_coding.fasta.gz
C_albicans_SC5314_A22_current_default_genomic.fasta.gz
C_albicans_SC5314_A22_current_default_protein.fasta.gz
C_albicans_SC5314_A22_current_not_feature.fasta.gz
C_albicans_SC5314_A22_current_orf_coding.fasta.gz
C_albicans_SC5314_A22_current_orf_genomic_1000.fasta.gz
C_albicans_SC5314_A22_current_orf_genomic.fasta.gz
C_albicans_SC5314_A22_current_orf_plus_intergenic.fasta.gz
C_albicans_SC5314_A22_current_orf_trans_all.fasta.gz
C_albicans_SC5314_A22_current_other_features_genomic_1000.fasta.gz
C_albicans_SC5314_A22_current_other_features_genomic.fasta.gz
C_albicans_SC5314_A22_current_other_features_no_introns.fasta.gz
C_albicans_SC5314_A22_current_other_features_plus_intergenic.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_chromosomes.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_default_coding.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_default_genomic.fasta
C_albicans_SC5314_version_A22-s07-m01-r179_default_protein.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_not_feature.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_orf_coding.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_orf_genomic_1000.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_orf_genomic.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_orf_plus_intergenic.fasta
C_albicans_SC5314_version_A22-s07-m01-r179_orf_trans_all.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_other_features_genomic_1000.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_other_features_genomic.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_other_features_no_introns.fasta.gz
C_albicans_SC5314_version_A22-s07-m01-r179_other_features_plus_intergenic.fasta.gz

I'm pretty sure I'd like to use the version *A22-s07-m01-r179* since it seems like it is a version that will is not transient like the *current* files.

QUESTION :

I am looking at bulk gene expression derived from an RNA-Seq experiment run on an Illumina sequencer. Which gff / fasta file should I use for alignment with hisat?

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  • $\begingroup$ What kind of sequencing did you do? Targeted? A gene panel? An exome? WGS? $\endgroup$
    – terdon
    Commented Feb 21, 2023 at 12:49
  • $\begingroup$ Just gene expression using rna-seq on an Illumina sequencer. Grinding up cells and getting the bulk gene expression $\endgroup$ Commented Feb 21, 2023 at 14:30
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    $\begingroup$ OK, please add that to your question, but make sure to actually explain what you are looking at. The file you need will be different if you're looking at all genes or specific genes. You can always use the main file with all chromosomes, but if you know you only care about 5 genes and all or on chr2, there is no point in using the whole thing. $\endgroup$
    – terdon
    Commented Feb 21, 2023 at 14:31

2 Answers 2

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First of all, you almost certainly want the current files. The convention in pretty much all sequence repositories is that foo.current is always the link pointing to the most recent and most up to date data. Those are what you want and not some "stable" version, you want the most accurate and that will usually be the current. In any case, my bet is that you will find that the *A22-s07-m01-r179* files are exactly the same as the corresponding *current* files since the current ones will just be symlinks.

Next, in order to align your data, you need the genome. The genome is this one:

C_albicans_SC5314_A22_current_chromosomes.fasta.gz

That is the file that has the chromosomes in fasta format, so that's the one you want for alignment. Now, if you have done RNAseq and only care about annotated, known genes, you could speed things up a little by using one of the more targeted files (just scroll down on the page you linked to for an explanation of what each file has), but using the whole genome won't be wrong. And at 8.4M compressed, that's a tiny genome so I don't think it's worth trying to get much more speed out of what will already be a pretty quick process.

As for which GFF, that will again depend on what you want, but most likely you want either of these, depending on whether you want GFF or GTF:

C_albicans_SC5314_A22_current_features.gff
C_albicans_SC5314_A22_current_features.gtf

The main message is that you usually want the "current" files, just make a note of what version the "current" files are pointing to if you need to report that.

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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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