As with SCGs, the proper breakdown of the capsid is paramount to guarantee the success in downstream analyses.
Expression profiling for 1/32 samples by DriverMap was not successful due to contamination, and it was not included in downstream analyses.
But if you have uncertainty, it'd be better to carry that forward and see what consequences it has in downstream analyses.
Intronic read counts were then divided by total intron length and total read count of the sample, to yield intronic RPKM that were used as a proxy of the transcription rate in downstream analyses.
Even small errors resulting from improperly selected or inaccurately used software tools or from ignoring the assumptions used by certain tools can have profound consequences in downstream analyses, potentially producing both false positive and false negative results.
To shed light on the impact of SEM in downstream analyses, we examined four representative applications.
The impact of this error in downstream analyses depends on the relative rates of error and real events of interest.
Here we examine the extent of sequencing error in these 2× assemblies, and its potential impact in downstream analyses.
It is also worth noting that indels at the ends of reads may not inhibit alignment and can in some instances be mistaken for SNPs in downstream analyses.
In downstream analyses, we kept saturating coverage values to ensure a reliable comparison across platforms and to avoid differences due to stochastic variations of single base coverage.
By considering no sources of data other than the sequence itself, this strategy has the advantage of being easy to interpret and avoiding complex biases in downstream analyses.
