Sourcetracker manual/guide using QIIME2


(Christian) #1

I am wanting some help in finding any guides / helpful pipeline manuals for utilizing SourceTracker software with QIIME2. I cannot find any helpful guides when downloading Sourcetracker from Github. I’m Quite desperate and looking to collaborate with authorship to my current paper if I can be helped with this. I have pushed my way through understanding and running QIIME2 with basic knowledge with its helpful tutorials, But this is where my expertise ends.

Thanks,

Am out of time researcher: frowning_face:


(Mehrbod Estaki) #2

Hi @codea,
Souretracker is currently not supported in QIIME2 directly, meaning if you have already created your ASV/OTU table in QIIME2 you’ll have to export them in order to use SoureTracker elsewhere. Though I have never used this tool myself, I know that you can use Souretracker in R (example page here) and there is also a QIIME1 wrapper.
Have you used this tool before and are having compatibility issues with QIIME2 outputs or is this all new territory? In other words, can you tell us exactly what it is you are looking to do, what have you done to this point, and which step is obstructing you?
If this is just a compatibility issue, I recently posted a simple working solution to going from a DADA2 ASV table to a closed-reference OTU table compatible with BugBase, which is another tool used by the same group that made SourceTracker. I’m guessing (though don’t quote me on this) that the same solution should be able to get you an OTU table ready for use with SoureTracker.
Let us know and hopefully we can guide you to figuring this out.


(Christian) #3

Hi @Mehrbod_Estaki,
I havent created the ASV/OTU table yet. I still have no idea what that is exactly. I am completely new to sourcetracker. Call me a complete and utter novice if you will. I have no idea how to operate sourcetracker at all, and all i have done so far is install it to my system. Im unsure how to create this table as well.
I’m looking to compare a host of samples (~80) to my water sources (~10).

Im also happy to communicate offline / skype if interested in this collaboration. I have had no luck understanding the manual for sourcetracker, seeing as there was so much support for operating QIIME 2.

Thanks in advance.


(Matthew Ryan Dillon) #4

Just to clarify @codea - sourcetracker is not developed by the QIIME 2 team. Have you tried reaching out on their support channels to get some assistance?


(Christian) #5

I have with no avail. I do know that there are ways of using sourcetracker with QIIME 2, i just thought i would try the knowledge of the team on this forum first.


(Matthew Ryan Dillon) #6

@Mehrbod_Estaki posted a pretty solid suggestion — it looks like you need a feature table (“BIOM” table) to get started with sourcetracker. QIIME 2 has many ways to get that table, and they are all detailed in the user docs — https://docs.qiime2.org - have you had a chance to read through and do any of the tutorials there?


(Christian) #7

Hi @thermokarst. I have got a BIOM table file. So at least ive got that going for me :slight_smile:. I’ll connect with @Mehrbod_Estaki now to work further.
Thanks again for your help.