Backlash running through my sequence

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Backlash running through my sequence

Emmanuel Nnadi
Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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sample_1.fasta (5M) Download Attachment
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Re: Backlash running through my sequence

Carson Holt-2
I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

—Carson



On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <[hidden email]> wrote:

Hi all,
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence

Thanks


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
<sample_1.fasta>


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Re: Backlash running through my sequence

Fields, Christopher J

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:

 

cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'

>contig_134\

>contig_149\

>contig_158\

>contig_222\

>contig_316\

>contig_582\

>contig_634\

>contig_700\

>contig_741\

 

I’m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?

 

chris

 

From: maker-devel <[hidden email]> on behalf of Carson Holt <[hidden email]>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] Backlash running through my sequence

 

I would not just remove them. The fact they are there calls into question how they got there in the first place. If you generated this file yourself, you may want to intead use fasta_tool.

 

—Carson

 

 

 

On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <[hidden email]> wrote:

 

Hi all,

I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them

 I attached the sequence

 

Thanks

 


Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

<sample_1.fasta>

 


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MPI vs multiple instance for speed

Patrick Tran Van-2

Hi Carson,


1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?


2) I am trying to annotate a 1GB specie but it's superslow.

I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ?


Cheers,

Patrick Tran Van



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Re: MPI vs multiple instance for speed

Carson Holt-2
MAKER can coordinate parallelization under MPI in a way it can’t even with multiple simultaneous runs. Because processes can comunicate among themselves under MPI, MAKER can break larger contigs into chunks or even pull off individual steps and pass them onto another processor, then receive the results back from that processor. So multiple BLAST, RepeatMasker, Exonerate, and prediction processes can all run at the same time for the same contig. Then they all pass their result back to the parent process so it can produce output for that contig. MPI was chosen as the parallelization framework rather than threads because it works both within a single machine as well as across multiple machines, so you can scale up to hundreds of processes if needed.

—Carson


On Oct 18, 2017, at 5:47 AM, Patrick Tran Van <[hidden email]> wrote:

Hi Carson, 

1) I think I have read one of your post saying that running maker with MPI is faster than multiple instance, can you explain why ?

2) I am trying to annotate a 1GB specie but it's superslow.
I have filtered the transcriptome to speed up the process but do you have other suggestion to increase the speed ? 

Cheers,

Patrick Tran Van




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Re: Backlash running through my sequence

Marvin B Moore
In reply to this post by Fields, Christopher J
Those look suspiciously like the remnants of end-of-line control characters.  Since Windows, Mac OS X and Linux all use slightly different control characters to mark end-of-line I’d look at the upstream path of where your files come from and how they’ve been processed by you or others upstream MAKER (were they generated or processed on a MS or Mac server).  One bizarre example we’ve seen is that files that simply pass through an MS Outlook server as an e-mail attachment have had their end-of-line characters converted to MS format.  Good luck…

Barry

On Oct 17, 2017, at 1:11 PM, Fields, Christopher J <[hidden email]> wrote:

I agree with Carson, though my guess is any fasta converters will either fail on these characters as non-IUPAC, or will silently remove them.  Running them through a converter may not solve all the issues though, as the backslash also appears in the FASTA headers at the end of the line:
 
cjfields-imac:MAKER cjfields$ grep '>' sample_1.fasta | grep '\\'
>contig_134\
>contig_149\
>contig_158\
>contig_222\
>contig_316\
>contig_582\
>contig_634\
>contig_700\
>contig_741\
 
I’m curious, was this edited using any particular program prior to MAKER (or was this an amalgam of different files)?
 
chris
 
From: maker-devel <[hidden email]> on behalf of Carson Holt <[hidden email]>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] Backlash running through my sequence
 
 
—Carson
 
 
 
On Oct 15, 2017, at 3:32 PM, Emmanuel Nnadi <[hidden email]> wrote:
 
Hi all, 
I am trying to running annotation on some of my sequences but noticed that i have backslash that runs through the sequence. Please how do I remove them
 I attached the sequence
 
Thanks
 

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
<sample_1.fasta>
 
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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