Dear QIIME2 users, I need help in preparing my map file. The google spreadsheet available at QIIME2 page is ( https://chmi-sops.github.io/mydoc_qiime2.html) confusing. Can I merge the forward and reverse index sequence in the same column or do I want to feed in separate columns? I need help if anyone prepared a map file recently. Please inbox me.
Dear Guhankumar,
First of all, you please understand a concept that you have to feed the mapping file after merging forward (F) and reverse (R) reads of your individual sample. Do not provide any information of F and R reads in mapping file.
Once you receive the paired-end NGS data, following fundamental steps need to be followed in QIIME environment.
1. Evaluate the quality of obtained data.
2. Discard low-quality data.
3. Join the Read 1 and Read 2 to generate single assembled read for each sample.
4. Convert fastq files to FASTA files.
5. Now at this step, you need to copy all assembled reads into single folder and then feed your mapping file to the data.
Make sure that mapping file is to just categorize the NGS samples based on experimental conditions. I have herewith attached a mapping file for your understanding. Hope it will be useful for you.
Hello Guhankumar Ponnusamy ,
You can use my metadata file as template, but is un spanish.
I don't know from recognize that tutorial from the official Qiime2 webpage (https://docs.qiime2.org/2020.6/tutorials/metadata/)
Qiime2 is going to merge your R1 and R2 files based on the barcode. So you don't need to feed a barcode for each read, rather a barcode and index for each sample
Say ,Sample1_R1_AATT Sample1_R2_AATT,
Sample2_R1_ATTT Sample2_R2_ATTT
Should be on you medatada as,
Sample1 AATT
Sample2 ATTT
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