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Old 04-14-2016, 02:49 AM   #1
uselessAl
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Location: Dublinish

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Default Qiime

Hello there,
I am a life sciences masters student trying to get to grips with Qiime analysis. I am currently working with data from the literature (supplementary material) to try and replicate previous studies as a way of learning. I am at the point just before OTU picking. I have overlapped the forward and reverse sequences using join_paired_ends.py and I have manually made a mapping file. I am completely lost as to how to link my sequence data to my mapping file in order to get to the next step. I have completed the Qiime tutorials but this particular issue is not addressed in the tutorials. Any help would be great.
Cheers
Al
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Old 04-14-2016, 06:14 AM   #2
fanli
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The next step is to demultiplex your joined reads using a separate barcode file. The barcode sequences should match those in your mapping file.

see http://nbviewer.jupyter.org/github/b...tutorial.ipynb
Code:
split_libraries_fastq.py -o slout/ -i forward_reads.fastq.gz -b barcodes.fastq.gz -m map.tsv
you can replace forward_reads.fastq.gz with the fastq file output from join_paired_ends.py
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Old 04-15-2016, 02:14 AM   #3
uselessAl
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Excellent, thank you very much for your help.
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