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
=90left_max_read_len
=90left_reads_in
=24995053left_reads_out
=24994132right_min_read_len
=90right_max_read_len
=90right_reads_in
=24995053right_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
I see. I did not know that. I thought we can eliminate short reads only by trimmomatic (MINLEN). I did not know mapping tools also eliminate some reads.
Like always, thank you Devon
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.