Strange output from Homer findPeaks
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4.5 years ago
fr ▴ 210

I have ran Homer's findPeaks but I find the output to be strange. Even disregarding the column order (which seems messed up), it only shows 1 as every tag count? Could anyone tell me if there's something wrong? This is an ATACseq sample

# HOMER Peaks
# Peak finding parameters:
# tag directory = /path/to/my/TagDir/
#
# total peaks = 104711
# peak size = 100
# peaks found using tags on both strands
# minimum distance between peaks = 200
# fragment length = 50
# genome size = 2000000000
# Total tags = 12998914.0
# Total tags in peaks = 7515101.5
# Approximate IP efficiency = 57.81%
# tags per bp = 0.006499
# expected tags per peak = 0.650
# maximum tags considered per bp = 1.0
# effective number of tags used for normalization = 10000000.0
# Individual peaks have been stitched together into variable length regions
# FDR rate threshold = 0.001000000
# FDR effective poisson threshold = 4.441463e-07
# FDR tag threshold = 8.0
# number of putative peaks = 575167
#
# size of region used for local filtering = 10000
# Fold over local region required = 4.00
# Poisson p-value over local region required = 1.00e-04
# Putative peaks filtered by local signal = 0
#
# Maximum fold under expected unique positions for tags = 2.00
# Putative peaks filtered for being too clonal = 13
#
# cmd = findPeaks  /path/to/my/TagDir/ -o /path/to/my/out_file.txt -region -size 100 -minDist 200 -fragLength 50
#
# Column Headers:
#PeakID chr start   end strand  Normalized Tag Count    region size findPeaks Score Clonal Fold Change
chrM    21  6501    chrM-183    1   +
chrM    11006   16299   chrM-141    1   +
chr17   39843010    39848859    chr17-363   1   +
chr2    98666248    98667359    chr2-19 1   +
chr14   19415716    19419703    chr14-6 1   +
chr2    98662241    98662998    chr2-9  1   +
chr9    124422465   124426086   chr9-26093  1   +
chr4    95049750    95053652    chr4-25701  1   +
chr12   118300738   118302784   chr12-19855 1   +
chr7    44531167    44535185    chr7-9165   1   +
chrUn_JH584304  59493   60848   chrUn_JH584304-5    1   +

Thanks a lot in advance!

homer atac-seq • 1.2k views
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Entering edit mode

could you please show your homer command line please?

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