6254a2f3273acb0889ba875ffab273f0099cea16 galt Tue May 21 00:17:23 2019 -0700 Fixe problems found by htmlCheck validate and hgNearTest robot diff --git src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html index e8feabf..34eaa68 100644 --- src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html +++ src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html @@ -35,33 +35,33 @@ reads that overlap that position. (iv) The count distribution of heights is as follows from 1, 2, ...h, ...H-1, H: {n1, n2, ...nh, ...nH-1, nH; N = Σni (i = 1:H)}. For a particular height, h, the associated probability of observing a height of at least h is Ph = Σni(i = h:H) /N. (v) We computed the background frequency after randomly placing the same number of extended reads within the gene for 100 iterations. This controls for the length of the gene and the number of reads. For each iteration, the count distribution and probabilities for the randomly placed reads (Ph,random) was generated as in step (iv). (vi) Our modified FDR for a peak height was computed as FDR(h) = (μh + σh)/Ph, where μh and σh is the average and s.d., respectively, of Ph,random across the 100 iterations. For each gene loci, we chose a threshold peak height h* -as the smallest height equivalent to FDR(h*) < 0.001. +as the smallest height equivalent to FDR(h*) < 0.001. We identified FOX2 binding clusters by grouping nucleotide positions satisfying -h > h* and occurred within 50 nt of each other. +h > h* and occurred within 50 nt of each other.

For further details of the method used to generate this annotation please refer to Yeo et al. (2009).

Credits

Thanks to Gene Yeo at the University of California, San Diego for providing this annotation. For additional information on FOX2 CLIP-seq reads, please contact geneyeo@ucsd. edu directly.