Homer analysis result on -region output format error

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4.7 years ago

Jamie_Francesco • 0

Hi, all.

I am analyzing my ChIP-seq data with HOMER with various options but I just have some errors on output file.

I ran Homer (v4.11.1) with following command line on my linux server. (Ubuntu 18.04.1)

findPeaks homer_nosspe_shCon_pS5 -region -size 1000 -minDist 10000 -i homer_nosspe_shCon_input

All outputs of peaks.txt have proper outputs but ouptuts with -region option have some errors there.

One example of output, region.txt file looks like -

enter image description here

It is supposed that 12th and 14th column should have P-values according to header but it seems like that it does not match to its header. Is there anybody who have experienced this kind of mismatches?

ChIP-Seq Homer • 1.1k views

ADD COMMENT • link 4.7 years ago by Jamie_Francesco • 0

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Hi, Your 10th column header is not wrapped exactly and is spilling over to the 11th column. I think that's why you are getting confused with the headers.

ADD REPLY • link 4.7 years ago by Strand NGS ▴ 40

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I know that the 10th column of the header is long but all those header and entries are well tab delimited.

These are transposed header and the first line.

enter image description here

Still from 10th column to 15th column seems like mismatched with the header.

ADD REPLY • link 4.7 years ago by Jamie_Francesco • 0

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