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Old 02-22-2017, 07:12 AM   #4
fanli
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Location: California

Join Date: Jul 2014
Posts: 198
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Quote:
Originally Posted by rajesh1989 View Post
Report produced by tophat shows some other statistics

Left reads:
Input : 468668
Mapped : 443344 (94.6% of input)
of these: 216780 (48.9%) have multiple alignments (1 have >20)
Right reads:
Input : 468668
Mapped : 444468 (94.8% of input)
of these: 217699 (49.0%) have multiple alignments (1 have >20)
94.7% overall read mapping rate.
Aligned pairs: 433356
of these: 211726 (48.9%) have multiple alignments
5512 ( 1.3%) are discordant alignments
91.3% concordant pair alignment rate.
This says your input to tophat is only ~460k read pairs. This directly contradicts what you posted in the prep_reads.info. Are you sure you don't have mismatched files?
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