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Hello, I have 3 samples I'm working with. By comparing the total ONT sequenced read length and the estimated haploid genome sizes
sample 1: 24.96x coverage
sample 2: 22.36x coverage
sample 3: 22.47x coverage
after assembling the genomes, reducing them to haploid assemblies with Purge Haplotigs, and mapping the reads back on to the haploid assemblies using minimap2, I calculated the read coverage directly:
sample 1: 22.79x coverage
sample 2: 21.20x coverage
sample 3: 21.16x coverage
This all seems to agree with my initial calculations. The strange part is, when I create histograms of the coverage, sample 2 has one peak at 12x coverage. It had this peak before and after Purge Haplotigs and I'm not sure why it's so low. Sample 1 and 3 had 2 peaks originally- one at ~11 and another at ~22. After Purge Haplotigs, Sample 1 and 3 only had the haploid peak at ~22.
Can you help me understand what could have happened or simply why sample 2 had such a low coverage peak? Thank you for any guidance you can provide
The text was updated successfully, but these errors were encountered:
These are 3 separate species from the same genus. Sample 1 and 3 are closely related, but not sister species. Sample 2 is in the same genus, but in a different section. For the assembly sizes, these are before Purge Haplotigs:
sample 1: 1,076 MB
sample 2: 796 MB
sample 3: 1,082 MB
And these are the assembly sizes after Purge Haplotigs:
sample 1: 852 MB
sample 2: 776 MB
sample 3: 842 MB
These assembly lengths are close to the estimated haploid genome size calculated from flow cytometry:
sample 1: 875 MB
sample 2: 829 MB
sample 3: 869 MB
Hello, I have 3 samples I'm working with. By comparing the total ONT sequenced read length and the estimated haploid genome sizes
sample 1: 24.96x coverage
sample 2: 22.36x coverage
sample 3: 22.47x coverage
after assembling the genomes, reducing them to haploid assemblies with Purge Haplotigs, and mapping the reads back on to the haploid assemblies using minimap2, I calculated the read coverage directly:
sample 1: 22.79x coverage
sample 2: 21.20x coverage
sample 3: 21.16x coverage
This all seems to agree with my initial calculations. The strange part is, when I create histograms of the coverage, sample 2 has one peak at 12x coverage. It had this peak before and after Purge Haplotigs and I'm not sure why it's so low. Sample 1 and 3 had 2 peaks originally- one at ~11 and another at ~22. After Purge Haplotigs, Sample 1 and 3 only had the haploid peak at ~22.
Can you help me understand what could have happened or simply why sample 2 had such a low coverage peak? Thank you for any guidance you can provide
The text was updated successfully, but these errors were encountered: