Re: [Transdecoder-users] problems of installation

[<Ale...@cs...>]

It is possible that we find more than ORF in a contig - is there a reason you think that a mRNA assembly ought to be forced to only have one ORF? It is rare but assemblies can fuse genes. Would you prefer if the smaller ORF was not printed out (and therefore you wouldn't have the option of checking if it is real) ?

It is interesting that the name is the same. I guess this is not a Trinity assembly?

Brian?

________________________________
From: Zhang, Ning [Zh...@si...]
Sent: Saturday, 1 February 2014 2:01 AM
To: Papanicolaou, Alexie (CES, Black Mountain)
Cc: <tra...@li...>
Subject: Re: [Transdecoder-users] problems of installation

Yes, the name is identical, but the sequence is different.
Something like that:
>Ampelocissus_ele_scaffold99_Locus_33_4_22.4
MGQKNSTHSTMEENCKWHKLLPRERERLMGTVGRRAIRSKLKNCRAMEVGIAATIRDQNG
TD*
>Ampelocissus_ele_scaffold99_Locus_33_4_22.4
MDRQNSFHESFPRSYRGKQFPFLQGPNPILPGTSVCQPLLDPSSASGNGSGGQKMFSDGL
NRVISSDRALSLLSSPLPETQEIGLSSMVQQNPIPPAQTLIPSLHYTGLSQYASSQGMGD
SVGSILVSDGSSNANLHCPAIFQLGPDGSSTNSSHQTLSFSWE*

There are many cases in my .pep file.
Ning

On Jan 30, 2014, at 8:06 PM, <Ale...@cs...<mailto:Ale...@cs...>>
 <Ale...@cs...<mailto:Ale...@cs...>> wrote:

Are they duplicate (two identical proteins) from one contig or two proteins (different coordinates) in a contig?

A

--
Alexie Papanicolaou
CSIRO Ecosystem Sciences

________________________________
From: Zhang, Ning
Sent: Thursday, 30 January 2014 9:56:19 PM
To: Papanicolaou, Alexie (CES, Black Mountain)
Cc: <tra...@li...<mailto:tra...@li...>>
Subject: Re: [Transdecoder-users] problems of installation

Hi, all:
I found that there are some duplicate peptides in *.transdecoder.pep.
What happened? How can I get only one peptide for each contig, maybe the longest one.
Thanks
Ning
On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote:

yes, I made it.
After installing this module, it works.
If you use Transdecoder on cluster, you had better install the module at your own path.
A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help.
Ning
On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>>
 <Ale...@cs...<mailto:Ale...@cs...>> wrote:

It seems that you or your sysadmin will have to install the perl module:

$ cpan URI::Escape

If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin

Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle...
a

--
Dr. Alexie Papanicolaou

Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247
CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia

-- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744>
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-- Bioinformatics is also an experimental science
________________________________
From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>]
Sent: Saturday, 25 January 2014 6:06 AM
To: tra...@li...<mailto:tra...@li...>
Subject: [Transdecoder-users] problems of installation

Hi, all:
I installed the latest Transdecoder with the command "make", however, when I run it, I got error message.

Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15.
BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15.
Compilation failed in require at ./TransDecoder line 102.
BEGIN failed--compilation aborted at ./TransDecoder line 102.

what is wrong with my installation.
Thanks.
Ning Zhang

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