Creating SAF data table for featureCounts for viral RNA-Seq

Question

[lokraj2003]

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

Answer 1

[dbpzdbpz]

The "Chr" values in the annotations for featureCounts don't need to be chromosome names. They can be contig names or anything as long as the names coincide with the chromosome names in your SAM or BAM files (in the @SQ header lines and also the third column of the alignment results).

In your case, the contig that you mapped reads to is named "AY386263.1", and I guess that all the alignment results in your SAM or BAM files have "AY386263.1" in the third column. Hence, the values in the "Chr" column in your SAF annotation file should be "AY386263.1". The Gene ID is the name of the gene that is on the chromosome or contig.

[lokraj2003]

@dbpzdbpz I tired using accession number as Chr and it works. Thanks !