Amplification Bias - 2
This is a further look at the paper: Calibrating genomic and allelic coverage bias in single-cell sequencing by Zhang, et. al.
In particular we reproduce Figure 2a cited in our earlier post. The data set can be retrieved
as a bam file from SRA reference SRR1779331. The coverage
data can be extracted from chromosome 1 (which is the only contig that’s used for the graph) using samtools depth.
To compute the autocorrelation, after considering several techniques, we settled on exploiting the sparse matrix library from scipy. That is described in this post.
The figure we obtained does in fact reproduce Zhang:
