Entering edit mode
9.2 years ago
dixit.anirudha
•
0
Hi everyone,
I am using TopHat PE to align my RNA-sequences and in the alignment summary file I am finding this,
Left reads:
Input: 27176120
Mapped: 24040642 (88.5% of input)
of these: 715407 ( 3.0%) have multiple alignments (0 have >20)
Right reads:
Input: 27177333
Mapped: 23904080 (88.0% of input)
of these: 732099 ( 3.1%) have multiple alignments (0 have >20)
88.2% overall read alignment rate.
Aligned pairs: 22342472
of these: 20162 ( 0.1%) have multiple alignments
and: 22319633 (99.9%) are discordant alignments
0.1% concordant pair alignment rate.
Not sure what is going on. On the other hand the if I use either R1 or R2 files in TopHat SE, the alignment score is 95%. Any inputs to resolve this will be great. Appreciated.
Thanks a ton Devon.