Hi

I used TopHat to map my reads against their relative reference genome.

When I look inside prep_reads.info, I see:

• left_min_read_len=90
• left_max_read_len=90
• left_reads_in=24995053
• left_reads_out=24994132
• right_min_read_len=90
• right_max_read_len=90
• right_reads_in=24995053
• right_reads_out=24994422

Then when I open align_summary.txt, I see:

Left reads:
               Input:  24995053
              Mapped:  22715900 (90.9% of input)
            of these:   2106892 ( 9.3%) have multiple alignments (89 have >20)
Right reads:
               Input:  24995053
              Mapped:  22310498 (89.3% of input)
            of these:   2088630 ( 9.4%) have multiple alignments (148 have >20)
90.1% overall read alignment rate.

Aligned pairs:  21074559
     of these:   1469415 ( 7.0%) have multiple alignments
          and:    107380 ( 0.5%) are discordant alignments
83.9% concordant pair alignment rate.

In align_summary.txt I know the changes between "Input" number and "Mapped" is because some of reads are unmapped to reference genome. Ok.

But for prep_reads.info I do not know why _reads_out numbers are different from _reads_in numbers and if this difference is due to unmapped reads, why the difference is not equal to difference between the Input number and Mapped number in align_summary.txt?

       prep_reads.info        align_summary.txt
left   24995053-24994132=921  24995053-22715900=2279153
right  24995053-24994422=631  24995053-22310498=2684555