STARSolo detection of mitochondrial genes

[Eleni Stylianou]

I have mapped a GEO human single cell RNA seq dataset with STARSolo and after creating a Seurat object I cannot find any mitochondrial genes.

I checked my Aligned.toTranscriptome.out.bam.file after sorting it as follows,

samtools idxstats Aligned.toTranscriptome.out.sorted.bam | cut -f1 | grep -v MT | xargs samtools view -b Aligned.toTranscriptome.out.sorted.bam > MT_output.bam - this produced a 0.3GB file suggesting mitochondrial genes are present.

Can you please verify that STARSolo does detect human mitochondrial genes and that these would be in the Aligned.toTranscriptome.out.bam file? If so what would be the best way to quantify them?

Thank you very much.

Best,

Eleni

[Alexander Dobin]

Hi Eleni,

if the mitochondrial chromosome and genes are present in the genome FASTA and GTF files, STARsolo will quantify them.

I am not sure if your command will work to select mitochondrial reads, grep -v MT will *exclude* chromosome names that contain MT.

Cheers

Alex