I have called peaks using MACS2. Then I got a narrowPeak file like this.
1 4491713 4491913 testONE_peak_1 37 . 2.86003 3.72580 1.66717 80
1 4492782 4493153 testONE_peak_2 27 . 2.22933 2.71107 0.82442 242
1 4571554 4572026 testONE_peak_3 72 . 4.16005 7.21000 4.85200 282
1 4739486 4739879 testONE_peak_4 64 . 3.63128 6.42948 4.14394 275
1 4784848 4785061 testONE_peak_5 31 . 2.24218 3.19160 1.21569 133
Then I tried to visualize it in UCSC Genome browser and I got following error.
Error File 'testONE_peaks.narrowPeak' - Unrecognized format line 1 of file: 1 4491713 4491913 testONE_peak_1 37 . 2.86003 3.72580 1.66717 80 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
So I added chr to the chromosome column instead of 1 (Chromosome number).
chr1 4491713 4491913 testONE_peak_1 37 . 2.86003 3.7258 1.66717 80
chr1 4492782 4493153 testONE_peak_2 27 . 2.22933 2.71107 0.82442 242
chr1 4571554 4572026 testONE_peak_3 72 . 4.16005 7.21 4.852 282
chr1 4739486 4739879 testONE_peak_4 64 . 3.63128 6.42948 4.14394 275
chr1 4784848 4785061 testONE_peak_5 31 . 2.24218 3.1916 1.21569 133
When I tried to load the file again I got following error.
Error File 'testONE_peaks_NEW2.narrowPeak' - Error line 1 of custom track: thickStart out of range (chromStart to chromEnd, or 0 if no CDS)
Then I added following line to the top and I could load the file to UCSC Genome browser.
track type=narrowPeak name="Somite narrowPeak"
chr1 4491713 4491913 testONE_peak_1 37 . 2.86003 3.7258 1.66717 80
chr1 4492782 4493153 testONE_peak_2 27 . 2.22933 2.71107 0.82442 242
chr1 4571554 4572026 testONE_peak_3 72 . 4.16005 7.21 4.852 282
chr1 4739486 4739879 testONE_peak_4 64 . 3.63128 6.42948 4.14394 275
chr1 4784848 4785061 testONE_peak_5 31 . 2.24218 3.1916 1.21569 133
But the problem is I can not see anything in the Genome browser. Only the name is there. But nothing else. Do you know what I should do?