Hi!
We have sequenced up some single cells, but now I have to check the amount of rRNA/tRNA/chrM and how much coverage we actually have on known genes (per chromosome or something similar).
How do you people usually do this? I have been playing around with Igvtools count etc. But I want hard data i.e. 60% chrM reads and X reads on chr1 etc.
We only have 20 mill. reads per sample and only 8 samples. What is considered ok coverage with regards to genes we want to analyze (non-rRNA/tRNA/chrM)?
Thanks!
We have sequenced up some single cells, but now I have to check the amount of rRNA/tRNA/chrM and how much coverage we actually have on known genes (per chromosome or something similar).
How do you people usually do this? I have been playing around with Igvtools count etc. But I want hard data i.e. 60% chrM reads and X reads on chr1 etc.
We only have 20 mill. reads per sample and only 8 samples. What is considered ok coverage with regards to genes we want to analyze (non-rRNA/tRNA/chrM)?
Thanks!
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