text: user3886: 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?
  
  user298: 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.
  
original_text: 3886: <p>I downloaded the <a href="http://www.candidagenome.org/download/gff/C_albicans_SC5314/Assembly22/" rel="nofollow noreferrer">gff</a> and <a href="http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/" rel="nofollow noreferrer">fasta</a> files for candida albicans from <a href="http://www.candidagenome.org" rel="nofollow noreferrer">http://www.candidagenome.org</a>.  I want to use <code>hisat2</code> to align some fastq files against it.</p>
  <p>There are many files in each download :</p>
  <p>gff :</p>
  <pre><code>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
  </code></pre>
  <p>fasta :</p>
  <pre><code>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
  </code></pre>
  <p>I'm pretty sure I'd like to use the version <code>*A22-s07-m01-r179*</code> since it seems like it is a version that will is not transient like the <code>*current*</code> files.</p>
  <p>QUESTION :</p>
  <p>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 <code>hisat</code>?</p>
   298: <p>First of all, you almost certainly want the <code>current</code> files. The convention in pretty much all sequence repositories is that <code>foo.current</code> is always the link pointing to the most recent and most up to date data. Those are what you want and not some &quot;stable&quot; version, you want the most accurate and that will usually be the <code>current</code>. In any case, my bet is that you will find that the <code>*A22-s07-m01-r179*</code> files are exactly the same as the corresponding <code>*current*</code> files since the <code>current</code> ones will just be symlinks.</p>
  <p>Next, in order to align your data, you need the genome. The genome is this one:</p>
  <p><a href="http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/C_albicans_SC5314_A22_current_chromosomes.fasta.gz" rel="nofollow noreferrer">C_albicans_SC5314_A22_current_chromosomes.fasta.gz</a></p>
  <p>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.</p>
  <p>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:</p>
  <pre><code>C_albicans_SC5314_A22_current_features.gff
  C_albicans_SC5314_A22_current_features.gtf
  </code></pre>
  <p>The main message is that you usually want the &quot;current&quot; files, just make a note of what version the &quot;current&quot; files are pointing to if you need to report that.</p>
  