Tool to determine SARS-CoV2 reads in count matrix

Question

[universe_life]

Hi All,

Which tool we can use to determine the reads of SARS Cov2 in count matrix obtained at the end of analysis after we have aligned the raw FASTQ files with reference genome consisting both of Human and SARS CoV2 ? Any guidance would be highly appreciated.

Thank you.

[Arup Ghosh]

It won't be included in the count matrix if the reference assembly and the GTF file do not include SARS-CoV-2 details. Go for taxonomical classification of the FASTQ files using Kraken2.

[universe_life]

Hi, reference assembly and GTF File both include SARS-Cov-2 details. Is there anyway we can proceed ahead for the determination?

[GenoMax]

If GTF file includes those details they should already be showing up in your matrix. Is that not the case?

[universe_life]

I see! Thank you so much - I will pursue this line of thought!