Re: demultiplexing with fastq but without barcode read fastq

[Yoshiki Vázquez Baeza]

You can use split_libraries_fastq.py, note that the -b is an _optional_ option i.e. is not required. In your case if you use this script, remember to set --barcode_type as "not-barcoded".

Thanks!

Yoshiki.

[Colin Brislawn]

Hello Tonja,

Thanks for posting that excel file. It sounds like you need to make a metadata mapping file. This is a text file containing sample name, barcode, and other sample metadata, that you can use with this script. You can construct a qiime mapping file using the info in your excel file.

Take a look here:

http://qiime.org/documentation/file_formats.html#metadata-mapping-files 

Colin

[Colin Brislawn]

Hello Tonja,

I think you are right; demultiplexing is not quite working yet. Can you help me understand what input files you have? In your command you listed Pool1_18S.fastq. Does that one file have all your 18S samples, or is that just the 'Pool1' sample? 

Are these from the Illumina MiSeq or Ion Torrent? 

Thanks for telling me more,

Colin