How to set seed length

[dario.ka...@googlemail.com]

Dear all,

I am getting an error message from Trans–ABySS saying:

warning: the seed-length should be at least twice k: k=32, s=32

I have neither set a value for k (hence the default k=32), nor for for s, but considering the warning I would like to.

Could anyone tell me which flag to use for this?

And is there a complete user manual for Trans–ABySS 1.5.5 somewhere?

Cheers,

Dario

[Ka Ming Nip]

The seed size is set to `k' on purpose. It is not an error.

Ka Ming
--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]
Sent: March 13, 2017 6:31 AM
To: Trans-ABySS
Subject: How to set seed length

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[dario.ka...@googlemail.com]

Dear Ka Ming,

thanks for your reply!

So should I just ignore the warning I posted?

What about a user manual for version 1.5.5?

Cheers, Dario

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[Ka Ming Nip]

Hi Dario,

Yes, please ignore that warning message from ABySS.

We have a wiki on GitHub:
https://github.com/bcgsc/transabyss/wiki

Hope that helps!

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com]

Sent: March 16, 2017 6:08 AM
To: Trans-ABySS
Subject: Re: How to set seed length

Dear Ka Ming,

thanks for your reply!

So should I just ignore the warning I posted?

What about a user manual for version 1.5.5?

Cheers, Dario


Am Montag, 13. März 2017 19:02:40 UTC+1 schrieb Ka Ming Nip:
The seed size is set to `k' on purpose. It is not an error.

Ka Ming
--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: dario.karmeinski via Trans-ABySS [trans...@googlegroups.com<javascript:>]

Sent: March 13, 2017 6:31 AM
To: Trans-ABySS
Subject: How to set seed length

Dear all,

I am getting an error message from Trans–ABySS saying:

warning: the seed-length should be at least twice k: k=32, s=32

I have neither set a value for k (hence the default k=32), nor for for s, but considering the warning I would like to.

Could anyone tell me which flag to use for this?
And is there a complete user manual for Trans–ABySS 1.5.5 somewhere?

Cheers,
Dario

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[dario.ka...@googlemail.com]

Thank you very much for your help! :)

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