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EBI-Metagenomics / genome_uploader

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)
Apache License 2.0
20 stars 3 forks source link

What should I do if I don't have genome coverage? #2

Closed SilasK closed 1 year ago

SilasK commented 1 year ago

The genome coverage depends on the sample it is quantified. What should I put in if I don't have the coverage from the original sample?

Ge94 commented 1 year ago

Hi Silas, You should be able to compute genome coverage by aligning raw reads against each genome (e.g. with tools like bwa, bowtie2, BBMap...) and then extract coverage information with tools like samtools or BEDtools. As an alternative, some binners like metabat already generate this statistics in-house, therefore it might be found in the output files.

SilasK commented 1 year ago

I don't have the original samples anymore and didn't kept the internal files from metabat. I didn't found this information relevant to keep. as the coverage will be different in each sample..

Ge94 commented 1 year ago

Hi Silas, According to ENA guidelines, the preferred behaviour would be to have raw reads associated to genome assemblies. I know you are currently in contact with a colleague of mine about this, she is trying to sort this out with ENA helpdesk. As your case is quite exceptional, and it is unrelated to the scripts usage, I will close this issue and let my colleague work on this.