a problem with peak annotation after ChIP-seq

Question

[gpdus67]

Hi. I downloaded GEO data(GSE22276) and try doing downstream analysis. By the way I got a problem in the step of annotation with HOMER tool (annotatePeaks.pl). Input data is the output of previous step(in HOMER, it's findPeaks.pl) in the format of bed.

But result came out with annotation column blank, NA and same for following columns.

Input file has chromosome(chr1), start and end position in first three positions, which is necessary, I have no idea about why annotation failed.

Any idea for this?

Best wishes

Answer 1

[GouthamAtla]

toolannotatePeaks.pl takes a BED file and a genome file. Are you providing the proper genome file/name ? Check if the chromosome names are same ? Like 'Chr1' or '1' in both Genome and BED file ? Post the exact command used and first few lines of BED file.

[gpdus67]

I solved the problem. in bed file, chromosome names are like 'chr1' while '1' in genome and gtf files. I made them same and it works. I really appreciate your help. Thanks.

Answer 2

[Rituriya]

Hi All,

I'm facing similar issue from HOMER tool, reported by gpdus67. I have checked my peaks file and the genome file both have 'chr1' only. Still I always end up getting blank values in Annotated peak file. Is there anything to do with makeTagDirectory output? Command used:

./annotatePeaks.pl path-to-dir/peaks.txt hg18 > annotatedpeaks.txt

What am I doing wrong?

Peaks file also contains a lot of commented information in the beginning. Does it needs to be removed? Few lines from my peaks file:

#PeakID chr     start   end     strand  Normalized Tag Count    focus ratio     findPeaks Score Fold Change vs Local    p-value vs Local        Clonal Fold Change
chr1-1  chr1    91625448        91625674        +       258.5   0.584   378.000000      84.31   0.00e+00        0.49
chr1-2  chr1    154452940       154453166       +       255.1   0.597   372.000000      54.33   0.00e+00        0.49
chr1-4  chr1    121186277       121186503       +       214.0   0.561   314.000000      13.15   1.48e-225       0.54

I am tired of getting empty annotated peak file. Please help.

Thanks in advance.

[dally]

It must be removed, HOMER is peculiar about this.

Answer 3

[Guangchuang Yu]

you can try ChIPseeker.

Answer 4

[dcwest]

Hi gpdus67 and Rituriya, I'm not sure if this will help, but I had the same issue too--- I ended up needing to convert my .txt peak file from a Macs-based .txt file into an acceptable .txt file that annotate.pl could handle. So, in Homer, I did:

changeNewLine.pl path/peakfile.txt

I did this for all of my peak files... then it was able to annotate my stuff. Hope this helps! ~Diana