Re: [bedtools-discuss] Error in BEDtools getfasta

[Aaron Quinlan]

Hi,

Are you sure that there is no extra whitespace before the FASTA chrom label or before/after the BED chrom label.  The error is telling you that it cannot find "chr01" in your FASTA file.  While what you have pasted into your email suggests that this is crazy talk, whitespace undetected by the eye could be the issue.

- Aaron

quinlanlab.org

On Feb 7, 2013, at 12:34 PM, patricia...@gmail.com wrote:

Hi,

I am triing to use BEDtools to get some sequences from genomic coordinates. But I am having an errors saying " WARNING. chromosome (chr12) was not found in the FASTA file. Skipping." for each read that I have in my bed file.
I gave you some details about what I am doing.

I just download the last version of BEDtools (I think) bedtools-2.17.0.

Then I have 2 different files (much more longer that the little part that I show) :
* A fasta file with all the sequences of chromosomes

>chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

* a BED file with my genomic coordinates (already sorted)
chr01 187814 190840
chr01 307073 310104
chr01 701047 704068
chr01 702941 705962
chr01 702952 705972
chr01 867716 870740
chr01 914064 917087
chr01 991080 994104
chr01 1039795 1042815
chr01 1058713 1061736

And then I write the command line:
bedtools getfasta -fi all.con -bed 1-13_sorted2.bed -fo NewCandidates/Genomic_coordinates/1-13_1500.fa

The only thing that I get is "WARNING. chromosome (chr01) was not found in the FASTA file. Skipping." , thousands of times...

If someone can help me and told me what I am doing wrong, I will be very grateful.

Thank you all of you in advance.

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[Aaron Quinlan]

Would it be possible for you to send me (privately) links to your files?  I can then try to diagnose the problem.

- Aaron

quinlanlab.org

On Feb 14, 2013, at 2:55 PM, patricia...@gmail.com wrote:

Hi,

Thank you for your answer. No, I am not sure...but how can I be sure? I open both files with different viewer and I never saw any space. It can be because of the ">"?
If not, do you know another way to convert a gff file into a fasta file?

Thanks’ again!