Barcode/key file format for ddRAD-seq data
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Sarah Endenburg
Apr 4, 2016, 2:48:36 PM4/4/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hello,
I'm trying to use the UNEAK pipeline on Tassel version 3 to analyze ddRAD-seq data. However, I'm not sure how to format my barcode file. All the documentation I've read shows only one barcode sequence per sample. My data has two barcodes per sample (one per enzyme used in the double digest) as shown below.
Barcode1 Barcode2 Sample Column Row
CCGAATG CTAACGT AB-R-01-01 A 1
TTAGGCAG CTAACGT AB-R-01-02 A 2
AACTCGTCG CTAACGT AB-R-01-03 A 3
GGTCTACGTG CTAACGT AB-R-01-04 A 4
GATACCG CTAACGT AB-R-01-05 A 5
AGCGTTGG CTAACGT AB-R-01-06 A 6
CTGCAACTG CTAACGT AB-R-01-07 A 7
TCATGGTCAG CTAACGT AB-R-01-08 A 8
CCGAATG TCGGTACT AB-R-01-09 A 9
TTAGGCAG TCGGTACT AB-R-01-10 A 10
Will Tassel accept a key file with two barcode columns, or is there another way to format this so that it will run properly?
Thanks!
I'm trying to use the UNEAK pipeline on Tassel version 3 to analyze ddRAD-seq data. However, I'm not sure how to format my barcode file. All the documentation I've read shows only one barcode sequence per sample. My data has two barcodes per sample (one per enzyme used in the double digest) as shown below.
Barcode1 Barcode2 Sample Column Row
CCGAATG CTAACGT AB-R-01-01 A 1
TTAGGCAG CTAACGT AB-R-01-02 A 2
AACTCGTCG CTAACGT AB-R-01-03 A 3
GGTCTACGTG CTAACGT AB-R-01-04 A 4
GATACCG CTAACGT AB-R-01-05 A 5
AGCGTTGG CTAACGT AB-R-01-06 A 6
CTGCAACTG CTAACGT AB-R-01-07 A 7
TCATGGTCAG CTAACGT AB-R-01-08 A 8
CCGAATG TCGGTACT AB-R-01-09 A 9
TTAGGCAG TCGGTACT AB-R-01-10 A 10
Will Tassel accept a key file with two barcode columns, or is there another way to format this so that it will run properly?
Thanks!
Sarah Endenburg
Apr 5, 2016, 8:00:22 AM4/5/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
As well, are the flowcell ID and lane number essential for UNEAK to work? The company that sequenced my data didn't provide that information, and Stacks can demultiplex it using only the barcodes and sample IDs.
Matt C
Apr 15, 2016, 9:48:18 AM4/15/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
I have the exact same question. Please update if you learn anything! I will do the same.
Matt
Sarah Endenburg
Apr 15, 2016, 10:08:23 AM4/15/16
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Seemed to have gotten around the two barcode issue by listing all samples twice, once per barcode. Someone else did that here:
The flowcell ID should be in the first line of your Illumina files, if that's the kind of data you have. I found mine using the command: head -n1 * in the folder containing the raw files. I also e-mailed the sequencing company and got information about the lanes, but unfortunately it seems like Tassel just might not be suited to our data anyways. We were only using Tassel to obtain files in the correct format for Haplotag, so some colleagues are now trying to write a script that will allow us to use Stacks instead.
Hope that helps a bit :)
https://groups.google.com/forum/#!searchin/tassel/barcodes/tassel/4yXE1P0eEhY/GR6E_xBf60AJ
The flowcell ID should be in the first line of your Illumina files, if that's the kind of data you have. I found mine using the command: head -n1 * in the folder containing the raw files. I also e-mailed the sequencing company and got information about the lanes, but unfortunately it seems like Tassel just might not be suited to our data anyways. We were only using Tassel to obtain files in the correct format for Haplotag, so some colleagues are now trying to write a script that will allow us to use Stacks instead.
Hope that helps a bit :)
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