problem withe Illumina solexa sequencing

[g781]

hi all,

I have a dataset with 4 columns, inculde chromosome, position, read count and direction (F/R), extracted from original Illumina solexa sequencing dataset, but the dataset have highly redanduncy. The dataset is about ~130Mb. However, the dataset reduced to ~30M dramatically when I removed the redanduncy datas.

Whether the original dataset is wrong or nothing?

[NextGenSeq]

You want high coverage (which is what I think you mean by redundancy). Typically people shoot for at least 20x coverage for SNP and indel detection.

[g781]

The dataset is used to map the distrubution of nucleosomes in yeast genome. could I ask you whether the highly coverage dataset is able to map nucleosome distrubution.

I have used a template filtering program, published from Genome Res. 2010 Jan;20(1):90-100, to map the distrubution of nucleosomes. My condition is normal as wild-type, so typically the result should be the same with figrue 3D (yellow). However, the result is different the figure 3D (see yellow). Therefor, I doubt whether the highly coverage dataset is the cause of making results inconsistent.

My result is following:
http://140.116.247.56/g781/tss.jpg

[Nik]

I'm not sure what you really mean but I've had something similar and this was due to duplications.