Add restriction enzyme MsII?

[Nina Schwensow]

Hi,

I was wondering if the restriction enzyme MsII could be added? I'd be happy to share some test sequencing data for trying.

MsII:
5' CAYN4RTG
3' GTRN4YAC

5' ---CAYNN   NNRTG--- 3'
3' ---GTRNN   NNYAC--- 5'

Cheers
Nina

[Nicolas Rochette]

Hi Nina,

I'm not sure. I think this issue happened in the past but I can't remember what the source was (I think it was user-data and/or parameter choice related, but I'm not sure anymore).

Could you send me the output of:

for bam in *.matches.bam ;do
    samtools view $bam 282
done | gzip &> c282.matches.sam.gz

Best,

Nicolas

On 10/16/18 4:28 AM, Nina Schwensow wrote:

Dear Nicolas,

A little while ago you have added the restriction enzyme MsII (MSL1), and all seemed to be running fine. You asked me to come back to you when other parts of the pipeline behave unusually.

Now it seems so: I just tried the gstacks part, and receive the warning 'WARNING: Some loci seemingly do not start with a cutsite; check your input reads.' (log file attached). I am not sure why I get this warning.

Is it possible that the new RE MSII cutting sites are currently not (yet) recognized by the 'gstacks' unit? I assume 'process_radtags', cstacks or sstacks should have given a warning if anything had been wrong with the cutting sites or catalog loci?

Or does this mean that something went wrong during the steps of the pipeline?

Is this something I need to worry about or will the program work just the same with and without the warning?

I'd greatly appreciate any idea you might have!

Cheers

Nina

Am Do., 23. Aug. 2018 um 17:06 Uhr schrieb Nicolas Rochette <roch...@illinois.edu>:

Hi Nina,

Thanks for letting us know! I'm glad it was useful. Let us know if you run in any weird issues with other parts of the pipeline.

Cheers,

Nicolas

On 8/23/18 2:35 AM, Nina Schwensow wrote:

Hi Nicolas,

It took us a while to go back to this but I have now extensively tested it and can confirm that all seems to works fine with the restriction enzyme MsII (MSL1).

If you would like to test yourself, please let me know. I am happy to send the sequences of a few individuals in case you would like to confirm yourself - otherwise I believe you can add it to RE list in the next release.

Sorry again for the slow response, I was in the field for a few months...

Cheers

Nina

2018-03-16 23:48 GMT+01:00 Nicolas Rochette <roch...@illinois.edu>:

Hi Nina,

Here's a modified source file that adds support for MslI. You will need to recompile Stacks after replacing the "src/renz.cc" file with this one.

Please confirm that it works as expected. If it does we will include the change in the next release.

Regards,

Nicolas

On 3/14/18 5:08 AM, Nina Schwensow wrote:

Hi Nicolas,

I little while ago you offered to add the restriction enzyme MsII (=MSL1) . How did that go?

Cheers

Nina

2018-02-02 18:44 GMT+01:00 Nicolas Rochette <roch...@illinois.edu>:

Hi Nina,

Yes, thank you. I must have been tired, I was looking for MS2 (msll) instead of MSL1 (mslI).

Nicolas

Nina Schwensow wrote on 02/02/2018 10:11 AM:

Hi Nicolas,

Thanks! Does one of these links help?

https://www.neb.com/products/r0571-msli#Product%20Information

http://www.thermofisher.com/order/catalog/product/ER2001

Cheers

Nina

Am 01.02.2018 um 17:41 schrieb Nicolas Rochette <roch...@illinois.edu>:

Hi Nina,

This one is a bit tricky but I'll see what I can do. Could you provide me with a reference link for this enzyme? I wasn't able to find it

Nicolas

--

Dr. Nina Schwensow

--

Dr. Nina Schwensow

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Dr. Nina Schwensow

[邓巧玲]

Hi Nicolas
When I tried the gstacks part, I also receive the warning 'WARNING: Some loci seemingly do not start with a cutsite; check your input reads'
How did you solve it in the end? I'd greatly appreciate your answer!