Question: 16s amplicon metagenomics - no mapping file?
0
gravatar for manekineko
3.4 years ago by
manekineko130
Bulgaria
manekineko130 wrote:

Hi,

I have from MiSeq FASTQ files, pair-end, of 16s bacterial amplicons. I want to start a metagenomics analysis and I have read that most of the time people use Mothur or Qiime.

But for example Qiime needs the FASTQ files and also mapping file. My case is that I have only the R1 and R2 pair-end files for each sample which are already demultiplexed (from MiSeq) with removed barcodes and primers.

So was wondering how can I proceed from what I have already?

Thanks

qiime mothur • 1.6k views
ADD COMMENTlink modified 3.4 years ago by agata88790 • written 3.4 years ago by manekineko130
1
gravatar for agata88
3.4 years ago by
agata88790
Poland
agata88790 wrote:

You need to make mapping file by yourself according to names of files, primers, barcodes etc.

Example of mapping file is below: http://qiime.org/_static/Examples/File_Formats/Example_Mapping_File.txt http://qiime.org/documentation/file_formats.html

Best,

Agata

ADD COMMENTlink written 3.4 years ago by agata88790

Thanks but in the case I do not know the primers and barcode (they are already removed from the company) how to do that?

ADD REPLYlink written 3.3 years ago by manekineko130

Here is an example from qiime:

Mapping Files Without Barcodes and/or Primers

In some circumstances, users may need to generate a mapping file that does not contain barcodes and/or primers. To generate such a mapping file, fields for “BarcodeSequence” and “LinkerPrimerSequence” can be left empty. An example of such a file is below (note that the tabs are still present for the empty “BarcodeSequence” and “LinkerPrimerSequence” fields):

#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of
#exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
PC.354 Control 20061218 Control_mouse__I.D._354
PC.355 Control 20061218 Control_mouse__I.D._355
PC.356 Control 20061126 Control_mouse__I.D._356
PC.481 Control 20070314 Control_mouse__I.D._481
PC.593 Control 20071210 Control_mouse__I.D._593
PC.607 Fast 20071112 Fasting_mouse__I.D._607
PC.634 Fast 20080116 Fasting_mouse__I.D._634
PC.635 Fast 20080116 Fasting_mouse__I.D._635
PC.636 Fast 20080116 Fasting_mouse__I.D._636

http://qiime.org/documentation/file_formats.html

Best, Agata

ADD REPLYlink written 3.3 years ago by agata88790
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