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  • Jun 24 23:41
    coveralls commented #3118
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    wasade on dev

    fix #3100 addressing @wasade request Merge pull request #3110 from a… (compare)

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    antgonza on dev

    fix #3054 (#3115) * disable "A… (compare)

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    antgonza commented #3115
Jose Navas
@josenavas
Hey guys if somebody is available we have a problem with the live system any kind of support will be appreciated
Greg Caporaso
@gregcaporaso
hi all, what’s the official qiita URL? I want to reference it in a paper I’m working on
Yoshiki Vázquez Baeza
@ElDeveloper
that would be qiita.microbio.me
Greg Caporaso
@gregcaporaso
thanks
Yoshiki Vázquez Baeza
@ElDeveloper
NP
Cale Seymour
@BassMakesPaste
Is there a way to download every biom file on Qiita with associated metadata and package them together? I've been scouring the site for a week or so and can't find anything.
Antonio Gonzalez
@antgonza
Not at the moment as you need to do it one by one. Note that we are working on RESTful interface to make this easier but this is still on the works.
Greg Caporaso
@gregcaporaso
hey qiita-ers, what’s the file type of a “preprocessed demux” file? and what is in this file? I’m trying to share data from a study with someone, and i want to give them the mapping file and post split libraries sequences.
Jose Navas
@josenavas
hey @gregcaporaso
the preprocessed demux file is an hdf5 file that contains the demultiplexed sequences in a per-sample basis. It is an alternative representation of a FASTQ which allows faster per sample access
Prior discussions with @wasade lead to also an alternative implementation of the OTU map using hdf5 that is going to work in conjunction with this implementation of the demux file. I still didn’t had time to code it, but I’m planning to do so during the following 2 weeks.
Greg Caporaso
@gregcaporaso
ok, thanks for the reply
i chatted with @antgonza about it this morning too. my recommendation is that what these files are is better documented - i was looking for demultiplexed sequence data (in fna.gz format) and that was the one i thought i wanted. i couldn’t open it with gunzip or unzip, but could tell that it was binary, so was pretty confused. he mentioned that you guys are re-doing that page, so sounds like the better documentation of this stuff is already in progress
Greg Caporaso
@gregcaporaso
qiita devs: i know i’ve asked this before, but the preferred url is qitta.ucsd.edu?
Jose Navas
@josenavas
Nope, the preferred url is qiita.microbio.me
Greg Caporaso
@gregcaporaso
thanks!
Jose Navas
@josenavas
Sure!
Bradley Stevenson
@bsteve1120
qiita devs, I would like to include some stats to a proposal (in which I plan on using qiita) that describe the growth in size of this database over the last year(s). Can anyone point me in that direction or throw some stats at me?
Antonio Gonzalez
@antgonza
Hi @bsteve1120, we currently don't have something like this but we think is a good idea. However, we need to discuss internally what will be the best info to have available. Anyway, I'm wondering if you have a deadline for this?
Bradley Stevenson
@bsteve1120
@antgonza, thanks for considering this. The proposal is due Feb 5th so if i had the information by the 3rd, it will likely make it in. I will be pitching this to an audience who might not be familiar with Qiita and i would like to make the case that it reslly is the best resource for meta analyses of sequence data across many studies. Thanks for considering this!
Antonio Gonzalez
@antgonza
@bsteve1120, I have added an issue about this (biocore/qiita#1636) and you can find some basic stats here (retrieved on 012916): https://www.dropbox.com/s/sdbh9wlh9d1lc0d/qiita-file-stats-012916.txt?dl=0. Hope this helps.
Bradley Stevenson
@bsteve1120
Thank you @antgonza! Are these values the total for each time period/month? I ask because the numbers fluctuate and I expected them to be cumulative. Not to worry, I can do the math, I just wanted to confirm. Thanks again!
Antonio Gonzalez
@antgonza
@bsteve1120 yes total for each month => you need to add them.
Bradley Stevenson
@bsteve1120
@antgonza figured as much but wanted to confirm. Thanks again!