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  • empyrean
    Member
    • Sep 2010
    • 52
    #1

    normalizing multicov output

    Hi..

    i used multicov to get read counts for specific genomic regions from different samples. Now, i would like to get expression values for those samples by normalizing the data. Can anyone suggest how i can proceed in doing that. i am attaching the sample output below

    HTML Code:
    Chromosome Name	Start	End	Strand	Sample 1	Sample 2	Sample 3	Sample 4	Sample 5	Sample 6
Gm01	75	93	+	0	0	0	0	0	0
Gm01	142	433	+	0	0	0	0	0	0
Gm01	42335623	42335702	+	631	84	42	76	98	112
Gm01	27758807	27763057	+	557	149	123	306	550	645
Gm01	50818678	50819255	+	529	264	120	11	102	64
Gm01	27753335	27757417	+	308	85	72	148	242	264
    Tags: bedtools, normalization, rna seq, small rna
  • TiborNagy
    Senior Member
    • Mar 2010
    • 329
    #2
    Why do not you use TopHat?

    Comment

    • empyrean
      Member
      • Sep 2010
      • 52
      #3
      Hi.. i have around million genome coordinates and i am not sure whether tophat can handle that many data points. Also, the genome coordinates vary from 20bp to 10kb regions.

      Comment

      • TiborNagy
        Senior Member
        • Mar 2010
        • 329
        #4
        It is depends on the computational resources. It is worth to make a try.

        Comment

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