Closed dluecke closed 1 week ago
Hello @dluecke ,
I see you figured out the plotting problem from the plot attached in your email.
Thank you for the response, good to know my interpretation wasn't totally wrong even if that's bad news for our data quality. We will re-sequence from fresh samples.
best,
David
Hello,
I'm working on a trio-binned assembly (haploid but including both sex chromosomes), and am using the merqury hapmers.sh tool to get some insight on the process. The resulting plot has the expected read-only, maternal, paternal, and shared distribution, but the pattern is different than the provided example plot, which shows the single peaks for both parentals and the shared diploid peak perfectly overlapped. In the version from my data the coverage position and heights for these peaks are all variable:
How would you interpret this difference? Is it just because we have a haploid+XY vs fully phased diploid assembly, or variable read depths? Or does this point to deeper problems in the trio-binning process?
Here are the submission script and output files, jic. merqury-trio_test.stderr.txt merqury-trio_test.stdout.txt merqury-trio_test.slurm.txt
Thank you for your insight!