Confused with macs has a same result when my input files are BED 3 and BED 5 format
so first i using BED 5 format which has a score column to call peak:
chr10 3101187 3101287 . 2 +
chr10 3101479 3101579 . 12 +
chr10 3108149 3108249 . 3 +
chr10 3108181 3108281 . 9 +
chr10 3112671 3112771 . 4 +
chr10 3112764 3112864 . 0 +
chr10 3113341 3113441 . 7 +
chr10 3117528 3117628 . 20 +
chr10 3120261 3120361 . 8 +
chr10 3121492 3121592 . 6 +
And then I using BED 3 which only contains chrom , start and end pos from the same file:
chr10 3101187 3101287
chr10 3101479 3101579
chr10 3108149 3108249
chr10 3108181 3108281
chr10 3112671 3112771
chr10 3112764 3112864
chr10 3113341 3113441
chr10 3117528 3117628
chr10 3120261 3120361
chr10 3121492 3121592
And my command line : macs3 callpeak --nomodel -g mm --extsize 100 -f BED -t -B -n
But for the peak file, I got the same result:
chr1 7237920 7238020 noscore_peak_1 19 . 3.73832 6.02411 1.91909 89
chr1 8944014 8944115 noscore_peak_2 64 . 6.60377 12.2782 6.40137 49
chr1 9350355 9350455 noscore_peak_3 31 . 4.6729 7.879 3.17432 72
And :
chr1 7237920 7238020 test_peak_1 19 . 3.73832 6.02411 1.91909 89
chr1 8944014 8944115 test_peak_2 64 . 6.60377 12.2782 6.40137 49
chr1 9350355 9350455 test_peak_3 31 . 4.6729 7.879 3.17432 72
so dose this mean the score column is useless ?
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