does anyone know how to compute total alignment from TopHat. I have 5 files marked file*****.log and they all have the following format:
# reads processed: 7069046
# reads with at least one reported alignment: 710849 (10.06%)
# reads that failed to align: 6227028 (88.09%)
# reads with alignments suppressed due to -m: 131169 (1.86%)
Reported 2269253 alignments to 1 output stream(s)
my reads were 50bp and Tophat divided these into segment lengths of 25bp.
# reads processed: 7069046
# reads with at least one reported alignment: 710849 (10.06%)
# reads that failed to align: 6227028 (88.09%)
# reads with alignments suppressed due to -m: 131169 (1.86%)
Reported 2269253 alignments to 1 output stream(s)
my reads were 50bp and Tophat divided these into segment lengths of 25bp.
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