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

  • $\begingroup$ According to the featureCounts documentation: "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." $\endgroup$ – neilfws Jul 30 '18 at 3:59

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