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Zero covered bases and mean coverage but non-zero reads mapping #162

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bck243 opened this issue Apr 7, 2023 · 0 comments
Open

Zero covered bases and mean coverage but non-zero reads mapping #162

bck243 opened this issue Apr 7, 2023 · 0 comments

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@bck243
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bck243 commented Apr 7, 2023

When I use coverm genome -m count to get total number of reads mapping, I see 7174 reads from a given sample map to a bin. But when I use coverm genome -m mean or coverm genome -m covered_bases I get 0. Is this a this just a matter of rounding (the total genome bin size is 4,208,222 bp)?

For raw counts I ran:

coverm genome --bam-files *.sort.bam -m count -o count_99.tsv --min-read-percent-identity 99 --min-covered-fraction 0 --genome-fasta-files /path/to/genomes/*.fa

For mean I ran:

coverm genome --bam-files *.sort.bam -m mean -o mean_99.tsv --min-read-percent-identity 99 --min-covered-fraction 0 --genome-fasta-files /path/to/genomes/*.fa

Thanks!

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