I am running checkm v1.2.1. I ran coverage for my bins but the output seems to drop some of the bins, particularly those that I expect to have high coverage and represent a major portion of each community? Essentially, the coverage table only shows one bin from one sample and not the other two. Am I missing something about how the coverage command works?
checkm coverage --all_reads -x fa bins/ checkm_coverage.tsv allreads_LS01_001_alignment_sorted.bam allreads_LS01_002_alignment_sorted.bam allreads_LS01_024_alignment_sorted.bam
I had roughly these results for each of my bam files:
Hello,
I am running checkm v1.2.1. I ran
coverage
for my bins but the output seems to drop some of the bins, particularly those that I expect to have high coverage and represent a major portion of each community? Essentially, the coverage table only shows one bin from one sample and not the other two. Am I missing something about how the coverage command works?checkm coverage --all_reads -x fa bins/ checkm_coverage.tsv allreads_LS01_001_alignment_sorted.bam allreads_LS01_002_alignment_sorted.bam allreads_LS01_024_alignment_sorted.bam
I had roughly these results for each of my bam files: