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Old 03-11-2014, 10:07 AM   #1
Location: USA

Join Date: Sep 2012
Posts: 41
Exclamation Problem running bedtools (fastFromBed)

Hi Everyone!
I have a gff file of the drosophila r5.48 genome, and the corresponding all chromosome fasta files.
I want to extract the DNA sequences into a fasta file based on the coordinates from the gff file. I have tried using the command 'fastaFromBed' using bedtools, and it starts running well, but then suddenly stops saying that it is "unable to find FASTA index entry for '2L'"
Can anyone please help me out on what I might be doing wrong?

The command I am using is:
fastaFromBed -fi dmel_all_chr.fa -bed dmel_all.gff -fo out.fa

I will appreciate any ideas and/or suggestions
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Old 03-12-2014, 05:23 AM   #2
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Location: Budapest

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I think there is a record in your GFF that contains a contig name that can not be found in your FASTA file. Remove this record.
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Old 03-18-2014, 11:06 AM   #3
Location: USA

Join Date: Sep 2012
Posts: 41

Thanks, I will try to look for it
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bedtools, fastafrombed

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