SICER Fragment size estimation

Question

[user230613]

Hi there,

This is my first time performing chip-seq analysis. I would like to use SICER to identify enriched domains from histone modification data. One of the input parameters that SICER requires is the fragment size. From the manual:

Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.

How can I calculate the fragment size?

Answer 1

[iraun]

There is a script inside SICER download folder, called fragment-size-estimation.sh , you can try to use it to estimate the fragment size. I would recommend you to read SICER users google group. There are some interesting posts like: https://groups.google.com/forum/#!searchin/sicer-users/fragment/sicer-users/pWF0GmYYAMM/IISEiBArg18J talking about fragment size estimation issue.

Hope it helps.