Closed DianaSpurite closed 9 months ago
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
Error | Source | Column | Row | Message |
---|---|---|---|---|
Schema Validation Error | 2 paired fastq | library_name | 2759 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | 2 paired fastq | library_name | 2762 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | 2 paired fastq | library_name | 2764 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | AmpliTaq Gold | library_polymerase | 2809 | 'AmpliTaq Gold' is not an accepted value. |
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link] |
ancientmetagenome-environmental_libraries.tsv
is valid
I'll leave a bunch of comments with information later today to help with reviewing process
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
Error | Source | Column | Row | Message |
---|---|---|---|---|
Schema Validation Error | 2 paired fastq | library_name | 2759 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | 2 paired fastq | library_name | 2762 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | 2 paired fastq | library_name | 2764 | '2 paired fastq' does not match '^[\S]+$' |
Schema Validation Error | AmpliTaq Gold | library_polymerase | 2809 | 'AmpliTaq Gold' is not an accepted value. |
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link] |
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_samples.tsv
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
When the species PR is approved the commit should become validated
For the reviewer(s):
SAMPLES:
For the reviewer(s):
LIBRARIES:
I looked for the information here:
Sanganji-A1-Tooth and Sanganji-A2-Tooth: https://pubmed.ncbi.nlm.nih.gov/27581845/ -> ENA -> supplementary information -> Listed protocol
Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth: https://doi.org/10.1016/j.jasrep.2017.12.025 -> ENA -> main text -> Listed protocol (Meyer and Kircher, 2010)
Augsburg-Tooth -> our records sample: "1343UnTal85"
Tenerife-011-Tooth; Tenerife-004-Tooth; GranCanaria-005-Tooth; GranCanaria-008-Tooth; Tenerife-012-Tooth; Tenerife-013-Tooth: https://pubmed.ncbi.nlm.nih.gov/29107554/ -> main text -> ENA
Tepos_35-Tooth: https://pubmed.ncbi.nlm.nih.gov/29335577/ unfortunately I didn't note this one for some reason..
Cueva_de_los_Lagos-Tooth: https://pubmed.ncbi.nlm.nih.gov/29531053/ -> main text -> ENA -> Kircher et.al protocol, age for this sample middle from the listed "late Bronze Age"
Yámana-Tooth: https: //pubmed.ncbi.nlm.nih.gov/29632188/ -> ENA -> suplement table
Vác-Mummy-Tissue: our records, sample "92-A1"
Chinchorro-Mummy-Bone and Pericues-BC28-Bone: https://pubmed.ncbi.nlm.nih.gov/26198033/ -> ENA -> supplementary information
Marseille-Tooth -> our records, sample "OBS107"
Barcelona-3031-Tooth -> our records, sample "Barcelona3031"
SLC-France-Tooth: https://pubmed.ncbi.nlm.nih.gov/30478041/ -> didn't note, unfortunately
Karolva-Tooth: https://pubmed.ncbi.nlm.nih.gov/31594508/ ->ENA -> supplementary information
Abusir1655-Tooth; Abusir1595-Tooth; Abusir1668-Tooth; Abusir1671-Tooth; Abusir1607-Tooth: https://pubmed.ncbi.nlm.nih.gov/32859198/ -> ENA -> main text -> listed protocols
Dacaozi-Tooth: https://pubmed.ncbi.nlm.nih.gov/32483115/ -> ENA -> main text -> listed protocols (36, 37)
Riga_Cemetery-Tooth -> our recoreds, sample "G701"
Chincha-UC12-12-Tooth; Chincha-UC12-24-Tooth; Chincha-UC8-8168-Tooth: https://pubmed.ncbi.nlm.nih.gov/32661160/ -> ENA -> main text -> protocol ref. 71 -> in that protocol ref. 2 & 3, not sure about polymerase for this sample
Chiribaya_Alta-Bone and El_Yaral-Bone-> our records samples "sample 54" and "sample 64", however, library treatment appeared to mismatch in our records and the Hodgkins 2023 supplement table. Main text in the original publication didn't state anything about treatment: https://pubmed.ncbi.nlm.nih.gov/25141181/
Peru-NA40-Bone; Peru-NA42-Bone: https://pubmed.ncbi.nlm.nih.gov/24568772/ -> ENA -> main text -> listed protocol (KAPA)
Pueblo_Bonito-Tooth: https://pubmed.ncbi.nlm.nih.gov/28221340/ -> ENA, layout listed as paired, but appears to be single is 3 of the libraries
Gniezno-Tooth: https://pubmed.ncbi.nlm.nih.gov/28609785/ -> ENA -> protocol Meyer and Kircher. ref. 73, I listed "single stranded" but was confused about it
Punta_Candelero-Tooth: https://pubmed.ncbi.nlm.nih.gov/31710665/ -> ENA -> protocol Meyer and Kircher, fastq assumed for this sample
Sample age and library treatment from Hodgkins 2023 UNLESS info comes from "our records".
Our records simply copied everything from archive information to download sizes.
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
Sample age calculated considering 1950 as the present time
Hi Diana, Thanks for doing this! I noticed a couple of things:
For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.
For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?
For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)
For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....
For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.
Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.
Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
Error | Source | Column | Row | Message |
---|---|---|---|---|
Schema Validation Error | HotStarTaq DNA Polymerase DNA | library_polymerase | 2870 | 'HotStarTaq DNA Polymerase DNA' is not an accepted value. |
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link] |
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
Hi Diana, Thanks for doing this! I noticed a couple of things:
For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.
For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?
For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)
For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....
For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.
Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.
Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!
I have addressed all these points, so I think it's good to go now. Thankfully, this issue was much easier than anticipated due to coordinates being available and James's suggestion to indicate exactly where in original publications the info could be found! Thank you both for your help along the process and with reviewing!
I am also requesting a review from you @alexhbnr as you are at it at the moment. This is already revised and there are comments and changes made. If you have a moment, could you please have a look and merge this also?
the sample(s?) excluded from the table here are previously sequenced
I will review it properly at the beginning of next week @DianaSpurite. I started reviewing it yesterday and realised that all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al. I have contacted @jfy133 about how we should handle the publication DOIs of the samples as the samples have been previously published (see Supp. Data Table 2). @jfy133 pointed me to check the previous publications that had the same issue, e.g. Bieker2020 and the Oetzi publication. I will do this next week.
all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al.
yes, that sound like my mistake, I mixed up at the beginning of working with this publication.
Thank you for looking into this, let me know if I can help.
Hi @DianaSpurite and @iseultj,
I went through your review and have a few questions/comments that I am not completely sure about:
Sanganji-A1-Tooth
and Sanganji-A2-Tooth
, you have listed that your polymerase that was used for the library amplification was HotStarTaq DNA
(see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up with HotStarTaq DNA
instead?Tepos_35-Tooth
, there is already an entry from the original publication, so I would suggest to copy the info from there.Dacaozi-Tooth
sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".If you could please check the first question, I would then approve the review and we can merge with the master branch.
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
- For the samples
Sanganji-A1-Tooth
andSanganji-A2-Tooth
, you have listed that your polymerase that was used for the library amplification wasHotStarTaq DNA
(see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up withHotStarTaq DNA
instead?
I had set it to 'Unknown' initially, exactly because they state two, and my competence level is rather low when it comes to the sequencing methods, so I corrected it according to the review.
- For the sample
Tepos_35-Tooth
, there is already an entry from the original publication, so I would suggest to copy the info from there.
I will check and do so.
- All references to the protocol "Meyer and Kircher, 2010" should have the "Phusion Hot Start High-Fidelity DNA" polymerase, as this is the one listed in their protocol.
Can you please confirm - does this mean for Deir-Rifeh; Cueva_de_los_Lagos and Punta_Candelero samples?
- For the
Dacaozi-Tooth
sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".
Will fix this too
If you could please check the first question, I would then approve the review and we can merge with the master branch.
@DianaSpurite for points 2 to 4, I should have already done this, so nothing to worry there at the moment. Thanks for clarifying question 1. I will wait for @iseultj's feedback and then go ahead.
Thanks @DianaSpurite for putting all the work in the first place. That was a beast of a publication to add to AMDir.
Hi, the HotStart Taq was my mistake - I was looking at their SM where they include the following as modifications to the Rasmussen protocol: A first round PCR was set up with Multiplex PCR kit (Qiagen) as follows: 5 µl DNA library, 25 µl Mix, 20-100 nM each Multiplexing PCR primer, and H2O up to 50 µl... I looked at the multiplex PCR (qiagen) handbook to find it, but to be honest I wasn't clear whether they used the HotStart Taq or the enzymes used in the Rasmussen paper - maybe Unknown is the best way forward? Sorry for neglecting this PR, and thanks so much to both of you for both doing all the work and finishing it off!
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
Adding Hodgkind2023 samples
Pull Request
This PR is for a
For the following list(s):
New Publication
Publication Information
This pull request is to add samples from the following publication(s):
This is to close #1109
Checklist
github-bot
)?@SPAAM-community/ancientmetagenomedir
?/assets/enums
, e.g. material or archive)? If so the corresponding PR is here: https://github.com/SPAAM-community/AncientMetagenomeDir/pull/1118