Ben J Woodcroft
Ben J Woodcroft
It seems you are running an out of date version, which is the cause. Try updating. -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT ________________________________ From: Sabrin2020 ***@***.***>...
Try making a new environment, or installing with `install coverm==0.6.1`
Hi, Thanks for the nice words. If you specify `--coupled` then you are inputting the reads, and CoverM will do the mapping for you (using minimap2 by default). If you...
Hi, Afraid not at this stage. Can I ask what the point of that is? If you are looking at a metagenome then maybe the coverage of the entire contig...
Hey, good point. It already works for `contig` mode. Should change.
Right, the code to implement this would mostly be around book-keeping i.e. which read sets go with each other, which mapping parameters for each, etc. Is there Rust code somewhere...
Hi, No problem. You are right for the currently released version. However, if you install the version by git clone'ing the current main branch, then you the options for this...
Hi Not sure, never tried. CovrerM won't remove mappings unless you specify filtering parameters which I imagine you haven't. Can you reproduce mappings outside of coverm using minimap2? Do you...
Thanks for the update - perhaps this is an argument for integrating bowtie2 as a mapper..
Hi, good question. Not currently, I'm afraid. These features are not used so much around in my lab, I'm curious to know what your use case is actually. Extracting all...