ENCODE Chip-Seq alignments information

Question

[chrys]

Hi Guys,

I am looking at some Chip-Seq datasets by ENCODE and I ran in a little problem. Since I want to look at some transposable elements I am trying to find out how ENCODE did their read alignments.

This is a little bit of a remote question but it seems there is little information how exactly the reads where aligned or what settings where used. The tools they used were quite easy to find but more detailed information are a little sparse.

I am quite new to sequence analysis and so I am not yet that familiar with everything. If I overlooked something terribly obvious I apologize but maybe somebody could give me a hint where to find such information or point me in the right direction.

[dariober]

No... I don't think this question at all trivial.

[chrys]

It seems detailed informations are buried deep somewhere. Maybe I will try contacting them and asking them directly.

[jotan]

You should be able to find the details of individual experiments on the GEO links (assuming the GEO).