smb20200615

@stefanogg thank you so much for your guidance. I had tried that but the issue with merging the variants is that we won't get the null calls - the approach...

has this issue been resolved? is there a way to fix it?

Hi Francisco, Thank you for your thorough comment. The reason I am struggling to make MAGs using your pipeline is because I don't have the account name for my cluster...

also sometimes these commands fail bash metaGEM.sh -t metabat -j 2 -c 24 -m 80 -h 10 bash metaGEM.sh -t maxbin -j 2 -c 24 -m 80 -h 10 (it...

sorry for the subsequent question. When I run refinement it still tries to rerun the samples that failed. I have been following the steps of the tutorial.

Thank you so much! That fixed it. I was wondering if the metabolic models were done just for the prokaryotic MAGs. Also, do you have guidance on how to adapt...

Sorry to build on that question. Is there anyway we can map positions of variants with respect to a publicly available reference genome?

It seems like a --vcf-ref is not an ordinary fasta file. So I cant use one of my genomes as a reference? ``` A fasta file with an entry for...

Yes, that is exactly my goal @iqbal-lab! Thank you for clarifying the issue about gene order. Do you foresee any issues with using tools such as Mauve to get the...

Of course! Thanks for working to address this.