Adapters problem

[Raistrawby]

Hello,
I’m working with the SQL-LSK 108 Kit and I have tried to add the adapter of this kit. However after including the new adapter in the adapter.py and start an analyze nothing happened, the new adapter wasn’t in the dialog box. I also try to modify the name of one adapter already in porechop and I have the same problem : the name hasn’t change.
I didn’t saw any other files to modify and I’m in the /Porechop/porechop/adapters.py.
Would you any idea how to solve my problem ? Alternatively, could you add the adapters if I provide you the sequences ?
Best regards,
Emma Corre

[laurafisch9]

Hi Emma,

I am trying to figure out the adaptor trimming for my minion data as well.
It looks like the SQL-LSK 108 kit adaptor sequences for both the Y adaptor and the 1D^2 are included in the adaptors.py file. However, it looks like the entire sequences has not been included and I am wondering why that is the case.
I think that albacore (or another base caller) trims off some of the adaptor sequences so in the fastq files output by a base caller will not have the entire adaptor sequence.
However, why not just include the entire adaptor sequence to ensure that porechop trims off the entire adaptor?

My main question is why would we not include the entire adaptor sequence for the Y adaptors and the 1D^2 adaptors in adapters.py?

Laura

[kdoroschak]

Just to clarify, the SQK-LSK108 adapter is identical to SQK-NSK007 already in adapters.py.

Not sure why it only includes the 2nd half, but I can confirm that it does properly remove the adapters from the SQK-LSK108 sequencing data I have.

[laurafisch9]

Hi Katie! Thanks so much for your response Can you tell me how you confirmed that porechop removed the entire adaptor? I am still new to bioinformatics work and am trying to get oriented with understanding sequencing data, Thanks Laura

…

On Wed, Jun 6, 2018 at 8:18 PM, Katie Doroschak ***@***.***> wrote: Just to clarify, the SQK-LSK108 adapter is identical to SQK-NSK007 already in adapters.py. Not sure why it only includes the 2nd half, but I can confirm that it does properly remove the adapters from the SQK-LSK108 sequencing data I have. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#64 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlF6tieMPY2lYONMdC9k40tmOw8lVlmhks5t6HFfgaJpZM4UWOS1> .

[snunzi]

I have the same question, why is only the second half of adapter included? Is this preferred over creating additional adapters with the entire sequence? Any insight would be appreciated!

[laurafisch9]

One reason could be that basecallers (we use albacore) ...I think will chop off parts of the adapters when they convert fast5 reads into fastq files

[Patrulk]

Hi,

Make sure you are editing the correct adapters.py. Depending on your installation Porechop might have installed in and use the one present in the python-dist directory. "/usr/local/lib/python3.5/dist-packages/porechop/adapters.py"

I see that this is a quite old thread but I had the same problem and maybe this info can be helpful to someone else.

Cheers
/Patrik

[LongYuan0529]

I also have this problem. I cannot get the right adapter.py to change. Where can I find it?
For “Which porechop”，I can only get the location of porechop "/Library/Frameworks/Python.framework/Versions/3.10/bin/porechop".

[Patrulk]

To get the path of an installed package you can run: python -c "import porechop as pore; print(pore.path)"

Depending on your system you might need to check which python was used for the installation and is called by the porechop executable, or else you might get a DistributionNotFound error.
You can check which python is used by opening the script you located using which and check the shebang at the top.

I.e:

1. cat /Library/Frameworks/Python.framework/Versions/3.10/bin/porechop
2. Check top line, should be something like "#!/usr/bin/python3"
3. Run /usr/bin/python3 -c "import porechop as pore; print(pore.path)"
4. The correct adapters.py should be in that folder

[ugh-astya]

Hello, I’m working with the SQL-LSK 108 Kit and I have tried to add the adapter of this kit. However after including the new adapter in the adapter.py and start an analyze nothing happened, the new adapter wasn’t in the dialog box. I also try to modify the name of one adapter already in porechop and I have the same problem : the name hasn’t change. I didn’t saw any other files to modify and I’m in the /Porechop/porechop/adapters.py. Would you any idea how to solve my problem ? Alternatively, could you add the adapters if I provide you the sequences ? Best regards, Emma Corre

Hi, Im using SQK LSK109. Im unable to find the adapter sequences anywhere online. Could you let me know where you found the adapter sequences for 108? Maybe I can do the same for 109.
Thanks

[ajneville]

Hello, I’m working with the SQL-LSK 108 Kit and I have tried to add the adapter of this kit. However after including the new adapter in the adapter.py and start an analyze nothing happened, the new adapter wasn’t in the dialog box. I also try to modify the name of one adapter already in porechop and I have the same problem : the name hasn’t change. I didn’t saw any other files to modify and I’m in the /Porechop/porechop/adapters.py. Would you any idea how to solve my problem ? Alternatively, could you add the adapters if I provide you the sequences ? Best regards, Emma Corre

Hi, Im using SQK LSK109. Im unable to find the adapter sequences anywhere online. Could you let me know where you found the adapter sequences for 108? Maybe I can do the same for 109. Thanks

Hello! Any luck with this yet? I just came access the issue and using SQK-LSK109 kit as well. I will try to dig into it as well. @ugh-astya - Thank you!