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  • Bedtools Intersection files

    Hello,

    I have a Splice Junction file in the tab delimited format and it looks like this:


    gravatar for ruchiksy
    1 hour ago by
    ruchiksy • 0
    Singapore

    Hello,



    I have a tab delimited format Splice Junction file and the file looks something like this:

    Code:
    chr1    11212    12009    1    1    0    0    2    48
    chr1    11672    12009    1    1    0    0    1    31
    chr1    11845    12009    1    1    0    0    1    28
    chr1    12228    12612    1    1    1    0    1    32
    chr1    12722    13220    1    1    1    0    3    9
    chr1    14830    14969    2    2    1    0    218    50
    chr1    15039    15795    2    2    1    0    98    50
    chr1    15948    16606    2    2    1    1    10    48
    chr1    16766    16857    2    2    1    0    24    44
    chr1    16766    16875    2    2    0    0    2    36
    The details are:

    Column 1: chromosome
    Column 2: first base of the intron (1-based)
    Column 3: last base of the intron (1-based)
    Column 4: strand
    Column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT
    Column 6: 0: unannotated, 1: annotated (only if splice junctions database is used)
    Column 7: number of uniquely mapping reads crossing the junction
    Column 8: number of multi-mapping reads crossing the junction
    Column 9: maximum spliced alignment overhang

    I want to create a intersection file using bedtools to find reads that have annotated junctions, unqiuely mapped reads and number of multi mapper reads equal to or greater than 10.

    I have not used Bedtools before so can I get some pointers on which command to use and how to input these parameters?

    Thanks!

  • #2
    Cross-posted on biostars, where it's already answered.

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