Re: help SAMMate2.7.4

[Tin Chi Nguyen]

Hi,

The major difference is that the new SAMMate also process junction reads and paired-end reads. Moreover, some bugfixes were done to SAM/BAM parser also. You can check the release note for more details.
Please tell me more details (SASeq/RAEM method, paired-end/single-end, etc), I can give more explanation.

Thanks

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From: "Roberta Spinelli" <spinelli...@gmail.com>
To: "Tin Chi Nguyen" <ex6...@wayne.edu>
Cc: dongx...@gmail.com
Sent: Friday, November 16, 2012 11:36:03 AM
Subject: Re: help SAMMate2.7.4

Dear all,

I'm comparing the gene expression obtained by SAMMate2.6.1 and SAMMate2.7.4.
I found many differences between them.
Why this divergences?

Is there an explanation?
This can be a problem.

Please, can you explain me why?

Many thanks,
Roberta

On Fri, Nov 16, 2012 at 5:19 PM, Tin Chi Nguyen <ex6...@wayne.edu> wrote:

Hi Roberta,

Our google group is here http://groups.google.com/group/asammate.

Currently the Linux version runs only by command line. The purpose is that it can process very large data on strong Linux server. It is easy to use,

sh SAMMate.sh -m <method> -a <.gtf> -i <input files> -o <output>

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From: "Dongxiao Zhu" <dongx...@gmail.com>
To: "Tin Chi Nguyen" <ex6...@wayne.edu>
Sent: Friday, November 16, 2012 8:47:46 AM
Subject: Fwd: help SAMMate2.7.4

Hi Tin, can you please help Roberta with it? Thank you!

On Fri, Nov 16, 2012 at 8:15 AM, Roberta Spinelli <spinelli...@gmail.com> wrote:

Dear Zhu,

many thanks.
But, How can I register to google group?

Sorry,
Roberta

On Fri, Nov 16, 2012 at 1:31 PM, Dongxiao Zhu <dongx...@gmail.com> wrote:

Hi Roberta, thanks for your interest. I am forwarding your email to the current developer Tin Nguyen. He can help with it and forward your email to google group.

Regards,

Sent from my iPad

On Nov 16, 2012, at 7:05 AM, Roberta Spinelli <spinelli...@gmail.com> wrote:

>
>
> Dear all,
>
> I will use SAMMate2.7.4, but my question is:
> in Linux can SAMMate2.7.4 run in a graphical way for gene expression or can
> it run only on command line?
> Why SAMMate2.7.4 in Linux doesn't output a report file?
>
> How can I send the emailto the google group?
>
> Best regards,
> Roberta from Italy
>
>