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?
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written
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user230613
1 answer
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.
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