Hello everybody !
I've run my first assembly recently and I'm trying to figure out its quality. I have honest n50 and a not so bad BUSCO of 80% complete busco. However, I am receiving mixed signals from Transrate and Bowtie2.
For both of them I have sent as input my trimmed fastq files and my final Trinity fasta. However, I got a 98 % overall alignment rate with bowtie2 but a p fragment mapped of 0.22 on Transrate that comes with a ridiculously low assembly score of 0.02...
I really want to say it is contradictory and forget the transrate thing, but it really makes me doubt .
Here is mybowtie2 output :
215513959 reads; of these: 215513959 (100.00%) were paired; of these: 33155696 (15.38%) aligned concordantly 0 times 47425197 (22.01%) aligned concordantly exactly 1 time 134933066 (62.61%) aligned concordantly >1 times ---- 33155696 pairs aligned concordantly 0 times; of these: 2974711 (8.97%) aligned discordantly 1 time* 30180985 pairs aligned 0 times concordantly or discordantly; of these: 60361970 mates make up the pairs; of these: 7085190 (11.74%) aligned 0 times 6679869 (11.07%) aligned exactly 1 time 46596911 (77.20%) aligned >1 times 98.36% overall alignment rate
Thank for your help