Closed iseultj closed 4 months ago
@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024
@spaam-bot please autofill ancientsinglegenome-hostassociated_libraries.tsv Jackson2024
@iseultj it needs to be the table name without _libraries.tsv
suffix, I realise now the terminology is unclear now π
@iseultj it needs to be the table name without
_libraries.tsv
suffix, I realise now the terminology is unclear now π
Oh cool! that makes sense π could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!
@iseultj it needs to be the table name without
_libraries.tsv
suffix, I realise now the terminology is unclear now πOh cool! that makes sense π could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!
I approved it, do you not have merge permissions?
@iseultj it needs to be the table name without
_libraries.tsv
suffix, I realise now the terminology is unclear now πOh cool! that makes sense π could you merge the other PR I made (#1162) so Streptococcus mutans is an allowed species? Thanks!
I approved it, do you not have merge permissions?
No, sorry!
Oh! Ok! Merged for you!@
@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024
All done - I think it might be better to get the ftp link for the submitted file rather than the file generated by the ENA/SRA though (which is what it does currently)- I have put ftp links and md5sums for the submitted files, because with the aligned bam, you get a generated fastq and have to realign anyway (which I assume people would prefer to go to the raw data for anyway). If you prefer the generated file, let me know and I'll modify it again :)
@spaam-bot please autofill ancientsinglegenome-hostassociated Jackson2024
@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024
@spaam-bot please autofill ancientmetagenome-hostassociated Jackson2024
@jfy133 I've made most of those changes - I don't think it really makes sense to treat them as one sample, given that when analysed there are 2 different genomes from each tooth, and if people want to include them in metagenomic analysis, each subsample of the tooth is pretty different. If you're ok with that, I think this is ready to merge - I have updated the dates and ftp links, and the automatically generated table is working well :)
AMDirT, version 1.5.0
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
Before merging - should I also add to single genome host assoc.? Raw reads & aligned bams available for T. forsythia and S. mutans (and bams aligned to T. denticola, but this is basically unusable in downstream analysis as is).
Pull Request
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This is to close #1160
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@spaam-bot please autofill <table_name> <project_id>
to get a half-filled template! (may take a minute or so to get the comment with the file)Pre-review checklist (new publications)
@spaam-bot please autofill <table_name> <project_id>
to get a half-filled template! May take a minute or so to get the comment with the file