16s amplicon metagenomics - no mapping file?
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5.6 years ago
manekineko ▴ 150

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

mothur qiime • 2.4k views
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5.6 years ago
agata88 ▴ 820

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

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

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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