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Old 02-03-2014, 12:18 PM   #1
empyrean
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Default 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
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Old 02-04-2014, 05:13 AM   #2
TiborNagy
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Why do not you use TopHat?
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Old 02-04-2014, 08:20 AM   #3
empyrean
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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.
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Old 02-05-2014, 03:28 AM   #4
TiborNagy
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It is depends on the computational resources. It is worth to make a try.
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bedtools, normalization, rna seq, small rna

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