Entering edit mode
3.9 years ago
Domu
•
0
I am working with Pseudomonas aeruginosa PA14 genomes. I aligned my Illumina reads to the reference genome using bowtie2 and when I look at the stats I get something like the following:
450261 reads; of these:
450261 (100.00%) were paired; of these:
191037 (42.43%) aligned concordantly 0 times
255656 (56.78%) aligned concordantly exactly 1 time
3568 (0.79%) aligned concordantly >1 times
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191037 pairs aligned concordantly 0 times; of these:
183325 (95.96%) aligned discordantly 1 time
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7712 pairs aligned 0 times concordantly or discordantly; of these:
15424 mates make up the pairs; of these:
5469 (35.46%) aligned 0 times
3976 (25.78%) aligned exactly 1 time
5979 (38.76%) aligned >1 times
99.39% overall alignment rate
I have read that concordant and discordant alignments are used to detect INDELS, however, 40% reads aligning discordantly seems very high. Can someone tell me what is going on?
Thanks in advance!
Did you trim the paired end data files independently? If so they are likely out of sync which will lead to highly discordant alignments.
No, I trimmed them in paired end mode of Trimmomatic
If you are willing, try aligning with
bbmap.sh
from BBMap suite and see what the stats say.should be all you need. Stats are written to STDERR.
Hey, thanks! I will look into this :)