compare distribution of coverage in solexa data

[scuellar]

Hi (i'm new in this forum and new in sequencing analysis, please be patient )

I’m comparing some solexa re-sequence experiment in which different DNA sharing treatment were used.

I there any statistic I can use to compare coverage evenness between sequencing experiments?

[drio]

Hi (i'm new in this forum and new in sequencing analysis, please be patient )

I’m comparing some solexa re-sequence experiment in which different DNA sharing treatment were used.

I there any statistic I can use to compare coverage evenness between sequencing experiments?

Assuming you have some ref sequence: Map your data with your aligner of choice and generate (S|B)am output. After that, pileup the alignments with samtools. Use column number 2 and 8 in the pileup to find out what's the reference coordinate and the number of reads covering the position. Then plot that with gnuplot (or R).

[scuellar]

Thanks Drio

Very helpful. Now i solved the problem the solutions sound so evident

Thanks again

[bioinfosm]

Or you could use something like IGV or USCS to visualize the coverage information.