PR for MAG fishing

[bioinfwithjudith]

This is a draft. I would like to add a description on the paper from where this data came from. I had some issues along the way and might be worth noting for new users.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.18%. Comparing base (1b9297b) to head (edb95cf).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #122   +/-   ##
=======================================
  Coverage   85.18%   85.18%           
=======================================
  Files          11       11           
  Lines        1080     1080           
=======================================
  Hits          920      920           
  Misses        160      160           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[dkoslicki]

Thanks! Let me know when it's ready for review

[bioinfwithjudith]

Updated description for README.md

Question:
NCBI accession: PRJNA924243 and has >50 MAG samples. Currently, the README.md instructs to concatenate these MAGS to work as input for YACHT.

• Should we keep as is?
• Would it be worth developing a script that runs YACHT on multiple MAG samples? (might need some direction for this)
• Should we just run it on one of these MAG samples?

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[dkoslicki]

Hmmm... @bioinfwithjudith I might need a bit more context. What do you mean by "50 MAG samples"? Do you mean MAGs derived from 50 different metagenomes, or 50 different assemblies from a single genome? If the later, then concatenating them would make sense if you wanted to answer "have any of these MAGs shown up in this other sample?", but keeping them separate would be "is this particular MAG occurring in this other sample?" So it just depends on what you are trying to answer

[bioinfwithjudith]

@dkoslicki

I see that I am confused.

The paper states "a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria" so I am assuming the latter.

I thought I was answering the MAG fishing question but I am not. Ideally, I would want to download the metagenomes sampled for this study, take a MAG and identify the metagenomes that have said MAG.

I have the MAGs downloaded but I am in the process of figuring out how to download metagenomic samples from MG-RAST.