 Dear bioc-sig-sequencing,

In running BioC2010 lab example, http://www.bioconductor.org/help/course-materials/2010/BioC2010/Workflow.pdf, comparing the "ctcf" lab example with my own chipseq Arabidopsis sample, results of the three available methods for estimate.mean.fraglen follow:

Method        ctest$ctcf(chr 10-12)       Arabidopsis sample(chr 1)

SISSR            192, 184, 196                 71

coverage         40, 40, 40                    195

correlation      0, 0, 0                         195


Seeing the variation in these results, decided to resize (page 3 of lab) Arabidopsis sample to 200 bp's (same as ctcf in lab).  Arabidopsis sample submitters report fragment size is 200-250 bp's.

Comparing page 17 & 18 strand specific coverage plots of "ctcf" lab supplied sample, and my Arabidopsis sample, I observed the following difference.

For "ctcf", see on page 17, 18 (and I can repeat running lab code), observe "skew" between strands with most of "area" of each strand separated by roughly insert distance of 200 bp's.

In contrast, for my Arabidopsis sample, strand specific areas roughly superimpose (line up) *without* having to adjust for estimated insert size.

Can someone comment on this observation?



Thanks,
P. Terry
pterry@huskers.unl.edu

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