How about using different Restriction enzymes with list of Stacks manual？

[Kang Yu]

Hi, there,

    I get the GBS paired-end data using a protocol that sequence DNA fragments cutting with a pair of restriction enzymes  SexAI and Sau3AI.

Here is my question: can process_radtags handle these data, sequences of  which start with barcode + SexAI  overhangs(CCWGGT) and its paired end sequences start with Sau3AI(GATC-3') ? What's your sugestions to process these kind of GBS data?

    Looking forward to your  reply. Thanks!

Kang Yu

[Julian Catchen]

Hi Kang Yu,

I can add these restriction enzymes to process_radtags if you are willing to
test them out. In the meantime, you can disable the rad site check in
process_radtags with the --disable_rad_check flag.

Best,

julian

[Kang Yu]

Hi, Julian,

Thanks for your reply. Could you add these restriction enzymes to process radtags?

 I want to test it on my data and split these paired-end GBS data into multiple samples for further analysis.

Thanks.

Kang

在 2013年4月23日星期二UTC+8下午2时36分43秒，Julian Catchen写道：

[Julian Catchen]

Hi Kang,

I have added the enzymes, please test them out for me before I release the code
publicly:

http://creskolab.uoregon.edu/stacks/source/stacks-0.99991.tar.gz

Best,

julian

On 5/8/13 11:07 AM, Kang Yu wrote:
> Hi, Julian,
>
> Thanks for your reply. Could you add these restriction enzymes to process radtags?
> I want to test it on my data and split these paired-end GBS data into multiple
> samples for further analysis.
> Thanks.
>
> Kang
>

> 在 2013å¹´4月23日星期二UTC+8ä¸‹å ˆ2æ—¶36分43秒，Julian Catchenå†™é “ï¼š

[Kang Yu]

Hi, julian,

I have another question. How to process data with barcodes which are in different length using process_radtags?

Thanks

Kang Yu

在 2013年5月10日星期五UTC+8上午3时24分02秒，Julian Catchen写道：

[Kang Yu]

Hi,

I test my data with process_radtags that you sent to me, but I got an message as follows:

Unrecognized restriction enzyme specified: 'sexAI'

my command:

process_radtags3 -i fastq -f test_1.fastq -o outfiles -b barcode -e sexAI -r -E phred33 -c -q  --barcode_dist 0

Kang Yu

在 2013年5月10日星期五UTC+8上午3时24分02秒，Julian Catchen写道：

Hi Kang,

[Julian Catchen]

Check that your install of the latest version (link below) succeeded. I am able
to select the sexAI enzyme here.

Barcodes need to be the same size for each end, but can be different between
ends. You can't mix barcode lengths for the same end, but you can run
process_radtags multiple times, once for each barcode length.

See the documentation here:

http://creskolab.uoregon.edu/stacks/comp/process_radtags.php

Best,

julian

On 5/10/13 2:42 AM, Kang Yu wrote:
> Hi,
>

> I test my data with process_radtags that you sent to me, but I got an message as
> follows:
> Unrecognized restriction enzyme specified: 'sexAI'
>
> my command:

> *process_radtags3 -i fastq -f test_1.fastq -o outfiles -b barcode -e sexAI -r -E
> phred33 -c -q --barcode_dist 0*
>
> Kang Yu
>
> 在 2013å¹´5月10日星期五UTC+8ä¸Šå ˆ3æ—¶24分02秒，Julian Catchenå†™é “ï¼š

>
> Hi Kang,
>
> I have added the enzymes, please test them out for me before I release the code
> publicly:
>
> http://creskolab.uoregon.edu/stacks/source/stacks-0.99991.tar.gz
> <http://creskolab.uoregon.edu/stacks/source/stacks-0.99991.tar.gz>
>
> Best,
>
> julian
>
> On 5/8/13 11:07 AM, Kang Yu wrote:
> > Hi, Julian,
> >
> > Thanks for your reply. Could you add these restriction enzymes to process
> radtags?
> > I want to test it on my data and split these paired-end GBS data into
> multiple
> > samples for further analysis.
> > Thanks.
> >
> > Kang
> >

> > 在
> 2013年4月23日星期二UTC+8下堈2时36分43秒，Julian
> Catchen写頓：

[Jeevan Adhikari]

Hi Julian,

I am working on PE libraries constructed with HinP1I and HaeIII. Could you also please add them?