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  • Tophat Exon -intron coverage

    Hi everyone
    i mapped my high quality reads on my reference genome using Tophat 2.0.7 ver. Now i want to know how many reads fall (mapped) in my exon and intron regions. and how many reads fall in intergenic regions. i stucked this place. Is anybody know how can i get exon intron and intrgenic reads mapping from my mapping file. Any suggestions will appreciate. Thanks in advance.

  • #2
    use intersectbed from bedtools https://code.google.com/p/bedtools/

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    • #3
      Thanks....... its works..

      Comment


      • #4
        Originally posted by mehtaaditya View Post
        Hi everyone
        i mapped my high quality reads on my reference genome using Tophat 2.0.7 ver. Now i want to know how many reads fall (mapped) in my exon and intron regions. and how many reads fall in intergenic regions. i stucked this place. Is anybody know how can i get exon intron and intrgenic reads mapping from my mapping file. Any suggestions will appreciate. Thanks in advance.
        hello,I want get exon intron and intrgenic file,how can i get this from tophat bam or bed file?Thank you

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        • #5
          Originally posted by mehtaaditya View Post
          Thanks....... its works..
          hello,I want to do the same work ! you can tell me more ?

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