prepare illumina fastq, extract barcodes

[heikieh]

Dear all,

I would like to analize illumina data (fastq) with the qiime pipeline.
However, in the tutorial for preparing the data I realized that for the split_libraries_fastq.py I need an extra fastq file for my barcodes.
I have found the extract_barcodes.py protocol. My problem with the protocol is that my sequences do not all start with the barcode.
Instead I have e.g. ACACTAG, NACACTGA, NNACAGATC or NNNACAGCTA and so on with N being the basepairs that are in front of the barcodes.
How could I best resolve this? How could I efficiently remove basepairs in front of the barcodes?
I would be really happy about any suggestions!

Heike

[Greg Caporaso]

Hello,

We don't currently have support for this, but are planning on adding it. You can follow progress here. Sorry for the inconvenience! 

Greg

[Tony Walters]

Heikieh,

Just to clarify the format of your sequences (for the above issue tracking that Greg opened), do your sequences look like this:

spacer of 0-X bases--Barcode Sequence--Primer Sequence--rest of amplicon read

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[Heike Staudacher]

Hello Tony and Greg,

yes they look like that, with 0-3 nucleotides before the barcode.

I will follow the progress with the link that you provided, thank you!

In think in my case it would be great if I could tell the program that my barcode are the 6 basepairs preceeding the primer sequence. This is not possible yet, right?

Thank you!

Heike

[Greg Caporaso]

Correct, that is currently not possible. Sorry for the inconvenience. 

Greg

[Sanjeev Sariya]

Hi Dr. Greg,

Pardon me to hack someone else's thread. 
May I know if there's any feature newly added by QIIME for the issue discussed ?

Best,

Sanjeev

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