I was wondering how do I convert a demultiplexed data into a mapping file that I can use in QUIIME?
Here is an example of how my data looks like in TextWrangler.
3056G_401 M02997:72:000000000-AW89G:1:1101:13437:1777 1:N:0:1 orig_bc=TTGCCAAGAGTC new_bc=TTGCCAAGAGTC bc_diffs=0
3056G_850 M02997:72:000000000-AW89G:1:1101:18541:1889 1:N:0:1 orig_bc=TTGCCAAGAGTC new_bc=TTGCCAAGAGTC bc_diffs=0
A metadata (“mapping”) file is for providing additional context and information to per-sample reads (or individual features) — that is usually some kind of data very specific to your particular study. For example, QIIME 2 sample metadata might include elapsed time, pH, elevation, surgery status, sample type, age, or body site. Check out the Metadata in QIIME 2 tutorial for suggestions on getting started with metadata. As well, take a peek at the Moving Pictures tutorial, which has a great example of a Sample Metadata file.
As far as importing your demultiplexed reads goes, please check out the Importing data section on Fastq Manifest formats - if your reads are already demultiplexed (per-sample), you can use this import type to get your reads into QIIME 2. Keep us posted and let us know if you have any questions!
Thank you for answering my question.
I was able to dowloaded the mapping file and check wether there are errors in it or not.
My question now is how do I download my sequences that have been already demultiplexed into QIIME2? is there an online link that shows one how to this?
and once downloaded, how do I check for chimeras?
I might be misreading this question, and if so please correct me, but this sounds like you are trying to import data. Please see my post above, there are links I provided to you above that provide references to importing these kinds of data.
Check out the Chimera filtering tutorial!
Before you jump into all of this though, I highly recommend you take a step back and review our Getting Started Guide — we have assembled several tutorials, plus a lot of general-purpose documents that explain how to get up an running with QIIME 2. Thanks!
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