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  • BED to sequence

    Is there a tool or code that will extract base sequence from a BED file?
    If a amplicon in a BED file covers 100 bases can I obtain that base information?
    I believe the coordinates are from ensemble. Thank you.

  • #2
    http://bedtools.readthedocs.org/en/l.../getfasta.html

    Comment


    • #3
      sequeence from BED

      Where do I use this command?

      getFastaFromBed -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo

      bedtools getfasta -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed

      I have Bedtools 2.17.0 and have the bed and fasta in the main directory. Thanks.

      Comment


      • #4
        Originally posted by cmccabe View Post
        Where do I use this command?

        getFastaFromBed -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo

        bedtools getfasta -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed

        I have Bedtools 2.17.0 and have the bed and fasta in the main directory. Thanks.
        Provided Bedtools executables are in your $PATH run the command like this. The output will be stored in the file called "output_fasta.fa" in example below (change name as needed)

        Code:
        getFastaFromBed -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo output_fasta.fa
        OR

        Code:
        bedtools getfasta -fi NS12911_noonan14.fasta -bed 14noonan.bed -fo output_fasta.fa
        If you need the sequences in Tab format then add -tab.

        Comment


        • #5
          sequence from BED

          I do not think I have the executable as I am gettig a bedtools not reconized.
          Do you know where I can get the exe.? I have attached a screenshot of the directory and in dos do a cd there first
          then use the command:

          bedtools getfasta -fi NS12911_noonan14.fasta -bed 14noonan.bed -fo output_fasta.fa - tab

          (the directory has the bed and the fasta in it as well but I removed them to decrease the attachment size). Thanks.
          Last edited by cmccabe; 07-16-2013, 12:06 PM.

          Comment


          • #6
            Oops .. we did not realize that you are referring to windows environment (based on your screenshot).

            Descriptions of the bedtools above were for Unix/Linux.

            I looked for windows versions and the one I see looked suspect so I am not going to link it here. Official releases of bedtools are only for unix/linux/os x.

            Do you have any experience with Unix/command line?

            Comment


            • #7
              sequence from BED

              Yes, we have ubuntu 10.0.4 and I think bedtools might be installed on there. Windows would be easier as the files are there, but I will confirm. Thanks

              Comment


              • #8
                You may be able to use Galaxy as well, which would allow you to keep everything on Windows.

                Link: https://main.g2.bx.psu.edu

                Comment


                • #9
                  Galaxy may be a good option as suggested by dnewkirk. bedtools should run quickly even on main galaxy.

                  Comment

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