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Old 03-03-2010, 04:19 PM   #1
scuellar
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Default compare distribution of coverage in solexa data

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

Im 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?
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Old 03-03-2010, 07:00 PM   #2
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Quote:
Originally Posted by scuellar View Post
Hi (i'm new in this forum and new in sequencing analysis, please be patient )

Im 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).
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Old 03-09-2010, 11:39 PM   #3
scuellar
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Thanks Drio

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

Thanks again
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Old 03-10-2010, 09:36 AM   #4
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Or you could use something like IGV or USCS to visualize the coverage information.
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