Question: Visualize smooth ChIP peaks with Homer makeUCSCfile
gravatar for varsha619
2.3 years ago by
varsha61980 wrote:

Hello, I am trying to use Homer makeUCSCfile for my ChIP seq data using as follows -

makeUCSCfile sample.tagdir/ auto -style chipseq > sample.bedGraph.gz

Although I am able to visualize the ChIP peaks in UCSC, I would like to get a smoothened plot instead, please let me know if there is an option that can be used to smoothen the peaks, Homer or otherwise. Thank you.

ucsc chip-seq homer • 1.1k views
ADD COMMENTlink modified 2.1 years ago by macmath140 • written 2.3 years ago by varsha61980
gravatar for macmath
2.1 years ago by
macmath140 wrote:

You can try check the below parameters Modifying Read Coverage You can manually set the fragment lengths that are visualized and shift their positions, both of which can be useful: -fragLength <# | given> : sets the fragment length, default: uses fragmentLengthEstimate in the tagInfo.txt file of the tag directory. If you want to visualize how the signal changes over large regions, it can be useful to set the fragment length to a very large value (i.e. 10000). If you want to visualize the exact length of the reads, use "-fragLength given".

-adjust <#> : adjust the position of the read by this amount from the 5' end. For example, -adjust -10 would start the coverage 10 bp upstream. This useful when the 5' end of the read represents a localized signal, i.e. DNase nicking site, as opposed to a ChIP-Seq fragment, which implies the factor binds downstream from the 5' end.

-tbp <#> : limit the number of reads considered per position, default: no limit. i.e. "-tbp 1" only counts one read per position.

-inputFragLength <#>, -inputAdjust <#>, -inputtbp <#> work the same for input directories if calculating a ratio.

ADD COMMENTlink written 2.1 years ago by macmath140
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