This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use Text Manipulation->Convert.

Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified).

All of the following will cause a line from the input dataset to be skipped and a warning generated. The number of warnings and skipped lines is documented in the resulting history item.

• Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
• Sequences that fall outside of the range of a line's start and end coordinates.
• Chromosome, start or end coordinates that are invalid for the specified build.
• Any lines whose data columns are not separated by a TAB character ( other white-space characters are invalid ).

What it does

This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.

If the output format is FASTA, the header format can be specified. Selecting the bedtools getfasta default option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and the "force strandedness" option is assumed. If the input data includes a strand column and the strand is '+' or '-', it is included in the header. If the input data includes a strand column and the value is anything but '+' or '-', a '.' is included in the header. If the input data does not include a strand column, a '.' is included in the header.

An example FASTA header produced by selecting this option is:

>chr7:127475281-127475310(+)

Selecing the character delimited field values option allows selection of a character delimiter that is used when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the selected character. For example, selecting an underscore will produce a FASTA header like this:

>mm9_53_550_+ test_chromosome

while selecting a vertical bar will produce a FASTA header like this:

>mm9|53|550|+ test_chromosome

If strand is not defined, the default value is "+".

Example

If the input dataset is:

chr7  127475281  127475310  NM_000230  0  +
chr7  127485994  127486166  NM_000230  0  +
chr7  127486011  127486166  D49487     0  +

Extracting sequences with FASTA output data type, character delimited field values as header format and header field delimiter set to the underscore character returns:

>hg17_chr7_127475281_127475310_+ NM_000230
GTAGGAATCGCAGCGCCAGCGGTTGCAAG
>hg17_chr7_127485994_127486166_+ NM_000230
GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
GATCAATGACATTTCACACACG
>hg17_chr7_127486011_127486166_+ D49487
TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
ACACG

Extracting sequences with Interval output data type returns:

chr7    127475281       127475310       NM_000230       0       +       GTAGGAATCGCAGCGCCAGCGGTTGCAAG
chr7    127485994       127486166       NM_000230       0       +       GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
chr7    127486011       127486166       D49487  0       +       TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG