Hi, I have manually created a bed file to extract the sequences from a fasta file. But it is showing the following error message. How can I solve it?
-bash-4.2$ cat pAcr_extract.bed
PSE305_1 20001 20479
PSE305_1 20306 20479
PSE305_1 20001 20303
AZPAE14907_contig_18_1 20001 20479
AZPAE14907_contig_18_1 20001 20303
WH-SGI-V-07178_contig3_1 20001 20303
WH-SGI-V-07178_contig3_1 20306 20479
bash-4.2$ bedtools getfasta -fi pAcr_extract.fasta -bed pAcr_extract.bed -fo pAcr_extract.fasta.out
It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?
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saadleeshehreen
bedtools is complaining about your file not being tab-delimited, try the following on your file if you have awk in your terminal to avoid making it again manually with tabs since I'm assuming its a big file:
cat pAcr_extract.bed | awk 'BEGIN{OFS="\t";} {print $1,$2,$3;}' > pAcr_extract_tab.bed
now try using bedools again with the newly created file in the -bed option.
Here a more general way for converting one ore more whitespaces into tabs using sed.
$ sed 's/ \+/\t/g' input > output
fin swimmer
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