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Old 06-16-2014, 10:58 PM   #1
bnfoguy
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Location: New Jersey, USA

Join Date: May 2011
Posts: 17
Post Bedtools Intersection files

Hello,

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


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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!
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Old 06-17-2014, 12:31 AM   #2
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

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