If you still have not received the VM email, your VM node URL is here: https://docs.google.com/spreadsheets/d/120pNr4uq_BVbRTWrqMs4heqtM8JuLgblzqNxIJCzWs0/edit?usp=sharing
Assuming you guys know this but thought I’d flag it anyway. (password for signing into the denbi node)
*Thread Reply:* You can click one ubuntu US/German
*Thread Reply:* Thanks @Chenyu Jin (Amend) ❤️
https://www.protocols.io/view/a-z-of-ancient-dna-protocols-for-shotgun-illumina-36wgq529xgk5/v2
*Thread Reply:* You mean why people use local over end to end/
*Thread Reply:* sensitive applies to both mode
*Thread Reply:* https://www.frontiersin.org/articles/10.3389/fevo.2020.00105/full This might help though, if you've not already read it
*Thread Reply:* Ah yes sorry, I meant local. Thank you for the paper!
*Thread Reply:* Note that our department are mostly BWA users (although the difference is quite small between the two)
*Thread Reply:* @Maxime Borry has some bowtie2 experience though
*Thread Reply:* @Rajiv Boscolo Agostini "end-to-end" is a global mode of bowtie2 alignment. In aDNA reserach, people prefer global alignment because it ensures the C/T polymorphisms are not soft-clipped as it is often the case for local (i.e. not "end-to-end") alignment. For the same reason people prefer "bwa aln" instead of more efficient "bwa mem", because the latter does local alignment which is not optimal for aDNA research. Basically, for aDNA applications, I would not run bowtie2 with local flag but only with end-to-end. Now, "sensitive", "very-sensitive", "fast" etc is not related (as far as I know, and as James said) to local-global choice but it is a special mode, i.e. a combination of low-level parameters which for simplicity was wrapped up under the "sensitive" flag
*Thread Reply:* Thanks @Nikolay Oskolkov!
*Thread Reply:* I wonder if you could write a short blog post on that @Nikolay Oskolkov? 😬 (@Ele and @Shreya)
Group 6 (@Erin E Barnett, @Luisa Sacristan, @Aurore Galtier & me) 🤡☕
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3429-6
*Thread Reply:* Uhhh that's interesting
*Thread Reply:* Gffread is what worked for me... There are various tools that should be able to sort the gff file I saw when googling it, maybe you can check for an alternative until I have a chance to fix it.
I can also send the gff file I prepared before maybe later or tomorrow.
Currently have to juggle baby and Ikea furniture 😅
*Thread Reply:* If you could find time to send the gff file you prepared I'd appreciate it
*Thread Reply:* And I'll also have a look into other tools as well in the interim
*Thread Reply:* This should have the entire dataset stuff for the pipeline session
*Thread Reply:* The gff should be in there
*Thread Reply:* Note the fine is 4.8gb!
*Thread Reply:* Because it contains the conda envs for aMeta,
*Thread Reply:* I've not had a chance to clean that up
*Thread Reply:* OK I'll make a note to clean it up after download, thanks for your quick response and help
Hi! I am attempting to set up the functional profiling environment on my institutions cluster and I ran into this error. Any ideas how to fix it?
*Thread Reply:* I think it's because it's been moved to bioconductor: https://www.bioconductor.org/packages/release/bioc/html/decontam.html
*Thread Reply:* Which mean it's now served in Conda Land by the Bioconda recipe rather than conda-forge
*Thread Reply:* Soooo replace that line in your conda.yml with: - bioconda:: bioconductor-decontam
*Thread Reply:* (not tested, from my phone )
*Thread Reply:* If it works let me know @Erin E Barnett then I can update the environment
*Thread Reply:* Thank you, @James Fellows Yates!
Ok final final thing! As above, the book above is only a draft and currently only contains the practical material.
But now, if you wish to recap any of the theoretical concepts from the morning lectures from @Christina Warinner @Meriam Guellil , Alexander Herbig, or myself, you can see these on YouTube!
https://www.youtube.com/playlist?list=PL3olEEj2ioAWPqnOglXhtTaMLb-j6KQHr
Unfortunately due to technical issues the quality of the recordings are low (Sorry about that 😞 ). But the quality of the audio and the slides should be good enough to read - and the slides are still on the summer school website (not the book!).
Happy ancient metagenomicking!
*Thread Reply:* Also @Christina Warinner @Meriam Guellil let me know if you see any mistakes - I did the uploads and info filling over a few days in spare moments so it wasn't a consistent workflow 🙈
*Thread Reply:* Awesome!! Thanks for all the things you've done😆