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  • Raw 16S Metagenomic data

    I have dual indices paired end sequences in separate fastq.gz files.
    Using EDAMAME's tutorial of using pandaseq I was able to join the paired end. However I do not understand how to do the Automated paired-end merging? Do I make the list as a txt file and save it in the same document? The shell script returns the error that the file in not found even if I drag and drop location of the file.

    Also, how do I extract the indices out?

    And, for the mapping file, Under Barcode Column, Do i combine both the indice? Under sample ID will it be separate for the forward and reverse strand?

    If there is A QIIME for dummies I would greatly appreciate it! :P

  • #2
    Hi,


    I'm not familiar with QIIME, but you can use the MOTHUR software package for that purpose. In addition you can avoid the use of pandaseq and start your analysis with your raw data fastq files.


    You may followed their SOP (http://www.mothur.org/wiki/MiSeq_SOP) and specific parameters to create contigs from paired end fastq files are found here: http://www.mothur.org/wiki/Make.contigs.


    Hope it help
    Last edited by vingomez; 02-23-2015, 08:17 AM. Reason: edit MOTHUR

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