Re: [bedtools-discuss] How to resolve error: WARNING. chromosome (Fvb0) was not found in the FASTA file. Skipping.

[Aaron Quinlan]

Hi Michael,

Could you email me (off the list) a minimal example BED and FASTA file that reproduces this problem?

Thanks,

Aaron Quinlan

Associate Professor 

Associate Director of the 

    USTAR Center for Genetic Discovery

Dept. of Human Genetics

Dept. of Biomedical Informatics

University of Utah

quinlanlab.org

aaronq...@gmail.com

On Apr 23, 2015, at 4:30 PM, Michael Alonge <malo...@gmail.com> wrote:

Hello,

I am trying to use bedtools -getfasta to extract sequences from a fasta file via a bed file.

fasta file:

>Fvb0

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

bed file:

Fvb0    1    100

Unfortunately I get the error described in the header for each line in the bed file.

This seems to suggest that my first column of the bed file does not match the headers of the fasta file, but this is not the case.

Not only do they match perfectly, but there is no white space either. I even made a test bed file with and exact fasta header name and coordinates and it still did not work.

Any help is appreciated.

Thank you

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[allyso...@gmail.com]

Hi,

I'm having the same issue as well. May I know how can I solve this? 

Thanks,

Allyson

[Aaron Quinlan]

Hi Allyson,

I would need small example files to attempt to recreate or resolve this problem for you. You can email me privately at aaronquinlan at gmail dot com

Aaron Quinlan

[Wong Yu Shiong]

It is solved. Thanks for reply.

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[Zhiyuan Liu]

How is it solved?

[Shaun Clare]

Would it be possible to get the fix for this since I am having the exact same issue. All chromosomes match, tab delimited bed file, no white space and still skips over all the features