2023_Salazar_MachuPicchu

[KathrinNaegele]

Check for existing package

I have checked the following places for the requested package and could not find
it:

• Poseidon Minotaur Archive
• The packages/ directory in this repository
• Open issues in this repository
• Open pull requests in this repository

Required information for the package

• DOI of publication: https://doi.org/10.1126/sciadv.adg3377 <- Please
  replace this example DOI with the one for the relevant publication
• Project accession number:
  PRJEB62808 <- Please replace
  this example ENA project link with the one for the relevant publication

Will you work on this?

If you are planning to work on compiling the .ssf file required to add this
package, please assign yourself to this issue. This helps the community
collaborate effectively and avoid duplicating work.

[stschiff]

@93Boy if you have capacity, I think this would be great if you could add an SSF file and create a PR, using the Project Accession code above.

[TCLamnidis]

Update: Processing is halted due to issues with the phred encoding of the ENA-converted FastQ files. Have contacted the ENA to get some clarity on the conversion process.

[TCLamnidis]

When BAM files with collapsed reads are uploaded to the ENA, three FastQ files are created from them containing the collapsed, R1 uncollapsed , and R2 uncollapsed reads respectively. Updated the pipeline to keep only the merged reads in those cases (which is generally a good idea for aDNA).
The merged reads have higher quality scores (since they are based on two observations), hence the error above. I update the package TSV and config accordingly and restarted processing.

[stschiff]

I thought you made a convincing point to map all three categories of reads? Was that not your final call? I think I'm fine either way.