manual

[galapah]

Hello,

I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed further. Can you please provide at least a sample sequence of commands?

Jan

[jandrewrfarrell]

This project is still under development, but you will find script files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected] wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers calculated
by Jellyfish. However, I am not sure how to proceed next. Can you please
provide at least a sample sequence of commands?

Jan

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[galapah]

Hi,

thank you for quick response!
I am sorry, I cannot see the RunRUFUS.HumanTrio.sh
http://runrufus.humantrio.sh/ even on GitHub:
https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell [email protected]:

This project is still under development, but you will find script files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected] wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers
calculated
by Jellyfish. However, I am not sure how to proceed next. Can you please
provide at least a sample sequence of commands?

Jan

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[galapah]

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala [email protected]:

Hi,

thank you for quick response!
I am sorry, I cannot see the RunRUFUS.HumanTrio.sh
http://runrufus.humantrio.sh/ even on GitHub:
https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell [email protected]:

This project is still under development, but you will find script files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh
should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected]
wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers
calculated
by Jellyfish. However, I am not sure how to proceed next. Can you please
provide at least a sample sequence of commands?

Jan

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[jandrewrfarrell]

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah [email protected] wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala [email protected]:

Hi,

thank you for quick response!
I am sorry, I cannot see the RunRUFUS.HumanTrio.sh
http://runrufus.humantrio.sh/ even on GitHub:
https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell <[email protected]
:

This project is still under development, but you will find script files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh
should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected]
wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers
calculated
by Jellyfish. However, I am not sure how to proceed next. Can you
please
provide at least a sample sequence of commands?

Jan

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[jandrewrfarrell]

do you have a reference for the plant your using? If so you will need to
change that in OverlapBashMultithread.sh to get a VCF. if you don't you
just want the mutant contigs you are all set

On Thu, Jun 16, 2016 at 2:45 PM, Andrew Farrell [email protected]
wrote:

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah [email protected] wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala [email protected]:

Hi,

thank you for quick response!
I am sorry, I cannot see the RunRUFUS.HumanTrio.sh
http://runrufus.humantrio.sh/ even on GitHub:
https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell <[email protected]
:

This project is still under development, but you will find script files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh
should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected]
wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers
calculated
by Jellyfish. However, I am not sure how to proceed next. Can you
please
provide at least a sample sequence of commands?

Jan

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[galapah]

Great! Thank your for the tips! It's Arabidopsis so I have a reference.

2016-06-16 22:46 GMT+02:00 J Andrew R Farrell [email protected]:

do you have a reference for the plant your using? If so you will need to
change that in OverlapBashMultithread.sh to get a VCF. if you don't you
just want the mutant contigs you are all set

On Thu, Jun 16, 2016 at 2:45 PM, Andrew Farrell <[email protected]

wrote:

yeah, tumor normal is what you should use for mutant vs wild type

On Thu, Jun 16, 2016 at 2:36 PM, galapah [email protected]
wrote:

I am running scripts/RunTumor.sh now.

2016-06-16 22:23 GMT+02:00 Jan Hapala [email protected]:

Hi,

thank you for quick response!
I am sorry, I cannot see the RunRUFUS.HumanTrio.sh
http://runrufus.humantrio.sh/ even on GitHub:
https://github.com/jandrewrfarrell/RUFUS/tree/master/scripts

I have reads from two plant individuals (mutant vs wildtype).

Jan

2016-06-16 22:11 GMT+02:00 J Andrew R Farrell <
[email protected]
:

This project is still under development, but you will find script
files
that should run everything in RUFUS/scripts/. RunRUFUS.HumanTrio.sh
should
run a trio analysis start to finish. What type of experiment are you
trying to run ?

On Thu, Jun 16, 2016 at 1:47 PM, galapah [email protected]
wrote:

Hello,

I am keen on trying this tool on our data! I already have kmers
calculated
by Jellyfish. However, I am not sure how to proceed next. Can you
please
provide at least a sample sequence of commands?

Jan

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