[maker-devel] Backlash running through my sequence

[Marvin B Moore]

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 <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> 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 <maker-devel-bounces at yandell-lab.org<mailto:maker-devel-bounces at yandell-lab.org>> on behalf of Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Date: Monday, October 16, 2017 at 11:22 AM
To: Emmanuel Nnadi <eennadi at gmail.com<mailto:eennadi at gmail.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
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 <eennadi at gmail.com<mailto:eennadi at gmail.com>> 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.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
<sample_1.fasta>

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