.. _getfasta: ############### *getfasta* ############### | .. image:: ../images/tool-glyphs/getfasta-glyph.png :width: 600pt ``bedtools getfasta`` extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file. .. tip:: 1. The headers in the input FASTA file must *exactly* match the chromosome column in the BED file. 2. You can use the UNIX ``fold`` command to set the line width of the FASTA output. For example, ``fold -w 60`` will make each line of the FASTA file have at most 60 nucleotides for easy viewing. .. seealso:: :doc:`../tools/maskfasta` ========================================================================== Usage and option summary ========================================================================== **Usage** .. code-block:: bash $ bedtools getfasta [OPTIONS] -fi -bed -fo **(or):** .. code-block:: bash $ getFastaFromBed [OPTIONS] -fi -bed -fo =========================== =============================================================================================================================================================================================================== Option Description =========================== =============================================================================================================================================================================================================== **-name** Use the "name" column in the BED file for the FASTA headers in the output FASTA file. **-tab** Report extract sequences in a tab-delimited format instead of in FASTA format. **-s** Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. *Default: strand information is ignored*. **-split** Given BED12 input, extract and concatenate the sequences from the BED "blocks" (e.g., exons) =========================== =============================================================================================================================================================================================================== ========================================================================== Default behavior ========================================================================== ``bedtools getfasta`` will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: ":-". .. code-block:: bash $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out $ cat test.fa.out >chr1:5-10 AAACC ========================================================================== ``-name`` Using the BED "name" column as a FASTA header. ========================================================================== Using the ``-name`` option, one can set the FASTA header for each extracted sequence to be the "name" columns from the BED feature. .. code-block:: bash $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 myseq $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out -name $ cat test.fa.out >myseq AAACC ========================================================================== ``-tab`` Creating a tab-delimited output file in lieu of FASTA output. ========================================================================== Using the ``-tab`` option, the ``-fo`` output file will be tab-delimited instead of in FASTA format. .. code-block:: bash $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 myseq $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out.tab -name -tab $ cat test.fa.out myseq AAACC ========================================================================== ``-s`` Forcing the extracted sequence to reflect the requested strand ========================================================================== ``bedtools getfasta`` will extract the sequence in the orientation defined in the strand column when the "-s" option is used. .. code-block:: bash $ cat test.fa >chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 20 25 forward 1 + chr1 20 25 reverse 1 - $ bedtools getfasta -fi test.fa -bed test.bed -s -name -fo test.fa.out $ cat test.fa.out >forward CGCTA >reverse TAGCG ========================================================================== ``-split`` Extracting BED "blocks". ========================================================================== One can optionally request that FASTA records be extracting and concatenating each block in a BED12 record. For example, consider a BED12 record describing a transcript. By default, ``getfasta`` will extract the sequence representing the entire transcript (intons, exons, UTRs). Using the -split option, ``getfasta`` will instead produce separate a FASTA record representing a transcript that splices together each BED12 block (e.g., exons and UTRs in the case of genes described with BED12). .. code-block:: bash $ cat genes.bed12 chr1 164404 173864 ENST00000466557.1 0 - 173864 173864 0 6 387,59,66,216,132,112, 0,1479,3695,4644,8152,9348, chr1 235855 267253 ENST00000424587.1 0 - 267253 267253 0 4 2100,150,105,158, 0,2562,23161,31240, chr1 317810 328455 ENST00000426316.1 0 + 328455 328455 0 2 323,145, 0,10500, $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name -fo stdout >ENST00000466557.1 gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattagcctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagcctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtgatggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggcagcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcctcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggccttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGTCCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctcctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGCAGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAATAATCATCATCT >ENST00000424587.1 ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggattacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGTAAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACATAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtccatctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatattaacaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgccctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGACAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGACAGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACAGTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagaccagcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaataagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATACTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGCATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCTCGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGAGGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCAGCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAAAGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggccgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagccccagctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtgagccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaaaaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAAGCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTTCCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTACAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTTTGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaactcttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgtgcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagttctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCTCTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTCTTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCAAAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG >ENST00000426316.1 AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgagagaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtatgagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGCAAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTTTGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTTGTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTTCCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATATTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA # use the UNIX fold command to wrap the FASTA sequence such that each line # has at most 60 characters $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name -fo stdout | \ fold -w 60 >ENST00000466557.1 gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggag ttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattag cctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatt tcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagc ctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGG GAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCA CCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTT CACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTT ACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtg atggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggca gcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcc tcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggc cttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGT CCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctc ctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGC AGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAA TAATCATCATCT >ENST00000424587.1 ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggat tacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGG CTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGT AAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTC TGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTT TATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGG GTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGT TTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATT TGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACA TAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtcc atctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatatta acaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgc cctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGA CAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGAC AGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACA GTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagacc agcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaat aagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATA CTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGC ATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCT CGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGA GGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCA GCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAA AGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggc cgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaacc ccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagcccc agctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtg agccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaa aaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAA GCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTT CCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAA GGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCA GCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTA CAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTT TGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaact cttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgt gcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagtt ctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCT CTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTC TTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCA AAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTC ATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG >ENST00000426316.1 AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgag agaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtat gagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGC AAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTT TGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTT GTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTT CCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATA TTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA