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  • lwhitmore
    Member
    • Aug 2013
    • 70
    #1

    Bedtools fastafrombed output

    Hey Everyone, I had a quick question about my bedtools fastafrombed output. When I get a sequence it contains both capital and lowercase letters. Does anyone know why it does this or what it means??

    Here is an example
    >chr1:157917-159078
    ATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAGGCACCTAGTAACAGCTCAGTAAATATTAGCTGCTACTATTATTATTTTTATGGTAATTTCACTCAATTAAAAACTGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAACAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgtataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataACACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgaggctgaggcaggaggattgcttgagcccaggaggttgaggctgcagtgagccataattgcaccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTTTTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAACTATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCGCAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGTGCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGACAGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCATTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactgggagactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtgaaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagtcccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgcagtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaaGacacacacaaacacacacacacacacacacacacCCCCAATCTCACTCTGTCCAGCCTTGACTAATCAAAAGGGCCTTCTG

    Thanks
    Leanne
    Tags: None
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    This could be reflective of exons in upper case and introns in lower case sequence, provided it was encoded that way. Something to check on.

    Comment

    • WhatsOEver
      Senior Member
      • Apr 2012
      • 215
      #3
      These are so-called soft-clipped repetitive regions.
      All lower case characters are thereby representing the repeats.

      You can reproduce this output using e.g. the Ensembl browser:
      -Input your coordinates
      -Click "Export Data" on the left
      -Choose repeat masked(soft) under fasta options (you will also find the possibility to create a hard clipped version there which will output all lower case characters as 'N')

      Comment

      • lwhitmore
        Member
        • Aug 2013
        • 70
        #4
        Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142
          #5
          Originally posted by lwhitmore View Post
          Hey when I try using the ensembl browser no matter which option I choose the sequence that is outputted is on N's
          Are you sure? I just go this from ensembl browser using your example (and WhatSOever's directions) in original post:

          Code:
          >1 dna:chromosome chromosome:GRCh37:1:157917:159078:1
AATAAGGAAGAATTATGGAGAATTTAAAAATCTATGCTATTTATAGGCACCTAGTAACAG
CTCAGTAAATATTAGCTGCTACTATTATTATTTTTATGGTAATTTCACTCAATTAAAAAC
TGTCGTTAAAAATTGCCATTGTCATGGAACATAATGTCTCCTACTGTATAATTGTAGAAA
CAGATACAATttgtcccttggtatatggggggattagttccagctctcccatttctgtgt
ataccaaaatccacgcatactcaagttttcaaagtcagtcctgtggaatccacatataAC
ACAAATGGGaaaattagtgaggtgtggtgacaagcacctgtagtcccagctacttgtgag
gctgaggcaggaggattgcttgagcccaggaggttgaggctgcagtgagccataattgca
ccactacactccagtctgggcaacagagtgagacAGAAGGTTGACTTTTTAATAGAATTT
TTCTGTTCACTTGAAGATATGGTCAGGATTGTGGCATATGAAAATTCTTCATAAAATAAC
TATCTAATCCAATTAATGCTGGAATTGGGAACAGCAGAAGTGTCATCTCAGAGCTACTCG
CAATGAAAGGTGATGTCTGGGGCTCAGGTGTGTTGAGGTCCCCATGCCTGGACTATGGGT
GCTGAGTGGGATTTACTTGTCCATCCATTTTCTATATTCCAGCACTGGGAAACTAGGGAC
AGTACTTGTTCTCAAGGGAATCTTCAGCTTAGGTGGCTCTGTAAAAGAGAAATTACATCA
TTGAAAAATCGTCGCAggtcaggtgaggtggctcatacctataatcccagcccactggga
gactaaggcaggaggattccgtgaggccaggagttcaagaccagcctgagcaacacagtg
aaacctcatctctacaaaaaattagaaaatgaactgggtgcggtaaaacattcgtatagt
cccagctactctggaggctgaaataggaggatcgcttgagcccaggaagtggaagctgca
gtgagctctgatctcaccactgcactctagccttggtgacagagtgagaccctgtctcaa
GacacacacaaacacacacacacacacacacacacCCCCAATCTCACTCTGTCCAGCCTT
GACTAATCAAAAGGGCCTTCTG

          Comment

          • lwhitmore
            Member
            • Aug 2013
            • 70
            #6
            Hey I got it , I guess I wasn't putting in the coordinates correctly

            Comment

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