Which sonicator did you use for your chromatin? Usually, it is very difficult to achieve such small inserts.
The seq facility is certainly correct that the size distribution is not optimal general purposes (small inserts generate redundant data). However, for ChIP-seq you only want to count and get the most precise mapping data possible. Shorter fragments give more precise data -- but only in case you can rule out sample degradation.
The seq facility is certainly correct that the size distribution is not optimal general purposes (small inserts generate redundant data). However, for ChIP-seq you only want to count and get the most precise mapping data possible. Shorter fragments give more precise data -- but only in case you can rule out sample degradation.
Originally posted by KB*
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