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xcor_header.txt 1.22 KiB
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See https://github.com/crazyhottommy/phantompeakqualtools for more details

COL1: Filename: tagAlign/BAM filename
COL2: numReads: effective sequencing depth i.e. total number of mapped reads in input file
COL3: estFragLen: comma separated strand cross-correlation peak(s) in decreasing order of correlation.
	  The top 3 local maxima locations that are within 90% of the maximum cross-correlation value are output.
	  In almost all cases, the top (first) value in the list represents the predominant fragment length.
	  If you want to keep only the top value simply run
	  sed -r 's/,[^\t]+//g' <outFile> > <newOutFile>
COL4: corr_estFragLen: comma separated strand cross-correlation value(s) in decreasing order (col2 follows the same order)
COL5: phantomPeak: Read length/phantom peak strand shift
COL6: corr_phantomPeak: Correlation value at phantom peak
COL7: argmin_corr: strand shift at which cross-correlation is lowest
COL8: min_corr: minimum value of cross-correlation
COL9: Normalized strand cross-correlation coefficient (NSC) = COL4 / COL8
COL10: Relative strand cross-correlation coefficient (RSC) = (COL4 - COL8) / (COL6 - COL8)
COL11: QualityTag: Quality tag based on thresholded RSC (codes: -2:veryLow,-1:Low,0:Medium,1:High,2:veryHigh)