<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>

CC BY-SA 4.0
2022-03-05T12:18:52.310Z
Cross-post here https://www.biostars.org/p/318489/
M__
CC BY-SA 4.0
2018-07-30T03:59:53.863Z
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."
neilfws
<r><bioconductor><covid-19><rna><virus>
How to create a SAF file for virus sequence?
# 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>

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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/  

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## 0 answers

