DNA de-novo assembly for plants different than rest organisms?
2
0
Entering edit mode
7.5 years ago
chefarov ▴ 140

Hello all,

I am using cloudbrush de-novo assembler in order to perform assembly on illumina reads from gardenia (plant). Following the same process which is successful for assembling E. Coli raw reads, it fails when I try to assemble on gardenia as I describe here (no useful debugging info).

Thus I was wondering if the procedure of de novo assembly from plants' raw reads differentiates from other organisms, in such a way that an assembler could fail in one case and succeed in the other.

Any thoughts?

de-novo-assembly dna-assembly plants • 1.8k views
ADD COMMENT
2
Entering edit mode
7.5 years ago
kmcarr00 ▴ 280

The data set you are trying to assemble (http://www.ncbi.nlm.nih.gov/sra/SRR1045129) is transcriptomic (RNA-Seq) data. You can not use this data for genome assembly.

ADD COMMENT
0
Entering edit mode

Thanks kmcarr00,

I can't believe my confusion :P

ADD REPLY
1
Entering edit mode
7.5 years ago
lomereiter ▴ 470

Most likely you've hit memory limit. Plant genomes are different in that they are much larger than bacterial ones (compare ~4.5Gbp of gardenia vs ~4.5Mbp of E.Coli).

ADD COMMENT
0
Entering edit mode

Thanks Iomereiter, I will try to firure it out.

ADD REPLY

Login before adding your answer.

Traffic: 1445 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