###參考：https://www.biostars.org/p/163356/

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

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?

The difference is due to filtering for things such as read length. Some reads are too short, so they‘re excluded. This occurs before any mapping takes place.

I seeeeeee. I did not know thaaat. I thought we can eliminate short reads only by trimmomatic (MINLEN). I did not know mapping tools also eliminate some reads.

Well, "things such as read length". It‘s filtering for other things too. In your case, one of these "other things" is what‘s causing additional reads to get dropped, since your input is all 90 bases

1、Question: prep_reads.info vs. align_summary.txt