Body: <p>I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by <strong>featureCounts</strong>. I need to create my own SAF. I tried making one but I am confused about the GeneID and Chr. The manual says Chr should match Chromosome number in the BAM or SAM file generated by <strong>align</strong> function. But viruses don't have chromosome. Could anybody help me with this please?</p>
  <p>Here is the link of the virus sequence which I am trying to create a SAF table for.
  <a href="https://www.ncbi.nlm.nih.gov/nuccore/AY386263.1" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/nuccore/AY386263.1</a></p>
  <hr />
  <p>Quoted from <a href="https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts" rel="nofollow noreferrer">R documentation website</a>
  <strong>featureCounts</strong> is a general-purpose read summarization function, which assigns to the genomic features (or meta-features) the mapped reads that were generated from genomic DNA and RNA sequencing.
  ... Both SAM and BAM format input files are accepted.</p>
  <p>...paraphrasing
  There is an in-built annotation that uses SAF format however <code>annot.ext</code> will override this for a custom SAF file.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-05T12:18:52.310Z
Comments.Text: Cross-post here https://www.biostars.org/p/318489/
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-30T03:59:53.863Z
Comments.Text: According to the [featureCounts documentation](https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts): "Users may also provide a GTF/GFF format annotation via annot.ext argument. But GTF/GFF annotation should only be provided as a file, and isGTFAnnotationFile should be set to TRUE when such a annotation is provided."
Comments.UserDisplayName: neilfws
Tags: <r><bioconductor><covid-19><rna><virus>
Title: How to create a SAF file for virus sequence?
ThreadText: # How to create a SAF file for virus sequence?
  
  (Asked by: username_0 on 2018-06-04)
  
  I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by **featureCounts**. I need to create my own SAF. I tried making one but I am confused about the GeneID and Chr. The manual says Chr should match Chromosome number in the BAM or SAM file generated by **align** function. But viruses don't have chromosome. Could anybody help me with this please?
  
  Here is the link of the virus sequence which I am trying to create a SAF table for.
  <https://www.ncbi.nlm.nih.gov/nuccore/AY386263.1>
  
  ---
  
  Quoted from [R documentation website](https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts)
  **featureCounts** is a general-purpose read summarization function, which assigns to the genomic features (or meta-features) the mapped reads that were generated from genomic DNA and RNA sequencing.
  ... Both SAM and BAM format input files are accepted.
  
  ...paraphrasing
  There is an in-built annotation that uses SAF format however `annot.ext` will override this for a custom SAF file.
  
  **Tags:** r, bioconductor, covid-19, rna, virus
  
  > **Comments:**
  > **username_2**: According to the [featureCounts documentation](https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts): "Users may also provide a GTF/GFF format annotation via annot.ext argument. But GTF/GFF annotation should only be provided as a file, and isGTFAnnotationFile should be set to TRUE when such a annotation is provided."  
  > **username_1**: Cross-post here https://www.biostars.org/p/318489/  
  
  ---
  
  ## 0 answers
  
  