Pre-processed BGI GBS data (barcodes removed)

[Laura Morales]

Hi,

I have a panel of near-isogenic maize lines (in B73 background with introgressions from NAM founders) that were sent for GBS sequencing at BGI. BGI has provided me with de-multiplexed, de-barcoded fastq files. Is is possible to use the GBSv2 pipeline without barcode information? More specifically, can the GBS database be built without the barcodes?

Thanks,

Laura 

[Lynn Carol Johnson]

Unfortunately, the current GBSv2 pipeline expects a barcode.

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[John Garbe]

I ran into this issue too, I've found that adding fake barcodes and quality scores to the demultiplexed/de-barcoded fastq files is a relatively simple workaround. You should also consider that Tassel is hardcoded to trim off a specific adapter sequence at the ends of reads. If BGI used a different adapter you'll have to trim it off yourself first before sending the data through Tassel.

[Laura Morales]

Okay, thanks Lynn. I will try the approach that John Garbe suggested.

On Thursday, February 8, 2018 at 2:40:11 PM UTC+1, Lynn Johnson wrote:

Unfortunately, the current GBSv2 pipeline expects a barcode.

 

From: <tas...@googlegroups.com> on behalf of Laura Morales <morales...@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Thursday, February 8, 2018 at 4:58 AM
To: "TASSEL - Trait Analysis by Association, Evolution and Linkage" <tas...@googlegroups.com>
Subject: [TASSEL-Group] Pre-processed BGI GBS data (barcodes removed)

 

Hi,

 

I have a panel of near-isogenic maize lines (in B73 background with introgressions from NAM founders) that were sent for GBS sequencing at BGI. BGI has provided me with de-multiplexed, de-barcoded fastq files. Is is possible to use the GBSv2 pipeline without barcode information? More specifically, can the GBS database be built without the barcodes?

 

Thanks,

Laura 

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[Laura Morales]

Thanks for the suggestion, John. BGI has refused to provide me with the raw multiplexed/barcoded fastq files because of proprietary reasons. Do you have a script for adding fake barcodes and quality scores that you would be willing to share?

[Tzu-Han Weng]

Hello, John, I also tried it by myself. I made fake barcodes and quality scores for all reads, and added in key file, but it couldn't be recognized by GBSSeqToTagDBPlugin. Could you please share the script or exchange the experience with me?

John Garbe於 2018年2月8日星期四 UTC+8下午11時57分49秒寫道：