Entering edit mode
23 months ago
Assa Yeroslaviz
★
1.8k
I have a follow-up question regarding my ONT data set, after my first question here. I have used minimap2 to map my sample against the reference genome and converted the results sam into bam file. I have than ran pycoQC with the addition of the bam files to check the alignments. I have attached below a few of the additional images added with the bam file QC run.
When I look at the pie chart I get only 0.14% unmapped reads, which would have been great, but when I look at the plot below, which shows the bases alignment rate, it shows ~70% reads unmapped. How do these two results fit together?
thanks
Is it possible to put the actual file up somplace? It is difficult to see things from this image.
yes, you can download it from the github repository.