HOMER annotatePeaks.pl 'Unique Peak ID' in first column changed in output file

Question

[theresa]

Greetings, I am able to run annotatePeaks.pl in HOMER on a ChIP-seq peak file, but in the annotated output, HOMER has changed my 'unique peak ID', which is problematic for downstream stuff I want to do. Can anyone help me? Problem detail below

I have a MACS ChIP-seq peak file ("PeakFile.txt") that I have formatted thusly:

Column1: Unique Peak ID
Column2: chromosome
Column3: starting position
Column4: ending position
Column5: Strand (+/- or 0/1, where 0="+", 1="-")

per http://homer.ucsd.edu/homer/ngs/annotation.html

Column1 entries read like so: peak1 peak2 peak3 peak4 ...

I am able to annotate the file with the following code in Terminal (Mac OS X):

checkPeakFile.pl PeakFile.txt ### all good

annotatePeaks.pl PeakFile.txt hg19 > annotatedPeakFile.txt

However in the resulting 'annotatedPeakFile.txt', the Column1 UniquePeak IDs read like so, sorted in ascending order as previously with the input 'PeakFile.txt

peak1 peak10 peak100 peak1000 peak10000 peak10001 peak10002

ugh. help please? I am a Mac OS user, and have saved my text .txt file in MS-DOS format as HOMER bucks Mac format. help appreciated

Answer 1

[theresa]

I am answering my own question here.

Used 'ChIPseeker' in R/Bioconductor to annotate my peak file. 'Windows-formatted' text is no longer available for Mac versions of MS Office, so HOMER might protest. ho hum.

https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html

Answer 2

[Prakash]

I think you need to format the format the peak file and then run annotatePeaks.pl you can follow this link to do the same C: how to keep column 6 (normalized tag count) in peaks.txt file called by Homer ca