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wwood / CoverM

Read coverage calculator for metagenomics
GNU General Public License v3.0
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Extract unmapped reads #62

Closed jsgounot closed 3 years ago

jsgounot commented 3 years ago

Hi,

first thanks for your tool, it's really usefull. I used coverm to determine MAGs abundance with my samples with options --min-read-aligned-percent 0.75 --min-read-percent-identity 0.95 and now would like to extract unmapped reads to explore what's are behind these reads. Is it possible ?

bests, jsgounot

wwood commented 3 years ago

Hi,

Thanks for your interest. I would suggest running genome mode with --bam-file-cache-directory to generate BAM files. Unfortunately, these BAM files have not been filtered for alignment thresholds. So, you would then have to run filter mode with the thresholding flags to unset the mappings. Then these sequences can be extracted from the BAM file with samtools.

Hope that helps. ben

jsgounot commented 3 years ago

Thanks, I overlooked the documentation and didn't see the filter mode. Will try that.

wwood commented 3 years ago

No problem.