Re: [stacks] Question about the formatting of barcode file with double digest data

[Nicolas Rochette]

Hi Juan,

If I understand your case properly, you barcode file should be in this form :

[sample1_barcode1] tab [sample1_barcode2] tab [sample1_name]
[sample2_barcode1] tab [sample2_barcode2] tab [sample2_name]
...

There are more examples and explanations in the manual : http://catchenlab.life.illinois.edu/stacks/manual/

Best,

Nicolas

Juan Enciso wrote on 08/02/2016 01:21 PM:

Hi, I'm quite new using stacks and I have a question about how to correctly format the barcode input.

My data comes from a double digest single-end assay and the barcode file I was given has the following format:

voucher barcode_name sequence
3500      bc_1                 CGATC
3500      bc_2                 AGTCC
...

As you can see, what I'm trying to show here is that there are repeated individual names with what appear to be two barcodes per individual, that, I guess, come from the two different enzymes used for the digestion. I just want to be sure about my guess because the format I'm using for this barcode file is:

CGATC 3500
AGTCC 3500

With repeated individual names in the second column and barcode sequences in the first one.
Does stacks<process_radtags> 'understand' that these are two different barcodes per individual and takes them both into account? Or, on the other hand, my barcode formatting is wrong and I'm producing spurious/unexpected results with this formatting?

The command line I'm using is:

process_radtags -p ./NS_SRobinson-NS12_BUTT_MID1x150V2_6-27-2016-31324302/BUTT-37549736 -b ./barcodes_elena_mod.txt -o ./out_radtags/ -c -q -r --renz_1 ecoRI --renz_2 mseI -E phred33 -i gzfast

demultiplexing by individual.

The results I'm obtaining are a single fastq file per individual.

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
---
You received this message because you are subscribed to the Google Groups "Stacks" group.
To unsubscribe from this group and stop receiving emails from it, send an email to stacks-users...@googlegroups.com.
Visit this group at https://groups.google.com/group/stacks-users.
For more options, visit https://groups.google.com/d/optout.