normalizing multicov output

[empyrean]

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

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

[TiborNagy]

Why do not you use TopHat?

[empyrean]

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.

[TiborNagy]

It is depends on the computational resources. It is worth to make a try.