Good bowtie2 alignment rate and low mapping on transrate ...
0
0
Entering edit mode
7 months ago

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

RNA-Seq Assembly software error • 347 views
ADD COMMENT
0
Entering edit mode

134933066 (62.61%) aligned concordantly >1 times 46596911 (77.20%) aligned >1 times

Most of your alignments fall into multiple locations, so, your reads are too short or you have a lot of repetitive sequences

ADD REPLY
0
Entering edit mode

Ok so I have many reads that map different places of my transcriptom. I know I had a lot of duplicates in my reads. Could it be an explanation ?

ADD REPLY

Login before adding your answer.

Traffic: 1028 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6