Question: SICER Fragment size estimation
1
gravatar for user230613
3.4 years ago by
user230613260
Europe
user230613260 wrote:

Hi there,
This is my first time performing chip-seq analysis. I would like to use SICER to identify enriched domainsĀ  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?

chip-seq • 1.7k views
ADD COMMENTlink modified 3.4 years ago by iraun3.5k • written 3.4 years ago by user230613260
1
gravatar for iraun
3.4 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

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.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by iraun3.5k
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