Hi all,
I recently got some RNA-seq data back that's left a bit puzzled. I opted for total RNA with rRNA depletion during library prep which was then sequenced using the Novaseq platform.
Of the resulting reads, there are some samples where only 30% of reads map to the nuclear genome - should this be expected?
I did some sleuthing and most unmapped reads map to the plastid.
I expected plant chloroplasts to feature prominently (given it is a leaf) but not constitute ~70% of my data.
Has anyone experienced this before? Was there a mistake made along the way?
I recently got some RNA-seq data back that's left a bit puzzled. I opted for total RNA with rRNA depletion during library prep which was then sequenced using the Novaseq platform.
Of the resulting reads, there are some samples where only 30% of reads map to the nuclear genome - should this be expected?
I did some sleuthing and most unmapped reads map to the plastid.
I expected plant chloroplasts to feature prominently (given it is a leaf) but not constitute ~70% of my data.
Has anyone experienced this before? Was there a mistake made along the way?
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