Visualize smooth ChIP peaks with Homer makeUCSCfile

Question

[varsha619]

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.

[Hamidreza]

Hi, could you solve this issue? I am also facing quite similar problem I guess. My problem is that using the BAM file, there are 2 separate but adjacent peaks in a region but TDF file merges them and shows them as a single peak. This problem also shifts the peak summit to the middle where in fact there is no summit. I attached an IGV screenshot here for a better understanding

Answer 1

[macmath]

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.