Question: DNA de-novo assembly for plants different than rest organisms?
0
gravatar for chefarov
4.9 years ago by
chefarov120
Greece
chefarov120 wrote:

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 usefull 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?

 

ADD COMMENTlink modified 4.9 years ago by kmcarr00270 • written 4.9 years ago by chefarov120
2
gravatar for kmcarr00
4.9 years ago by
kmcarr00270
United States
kmcarr00270 wrote:

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 COMMENTlink written 4.9 years ago by kmcarr00270

Thanks kmcarr00,

I can't believe my confusion :P
 

ADD REPLYlink written 4.9 years ago by chefarov120
1
gravatar for lomereiter
4.9 years ago by
lomereiter450
Russian Federation
lomereiter450 wrote:

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 COMMENTlink written 4.9 years ago by lomereiter450

Thanks Iomereiter, I will try to firure it out.

ADD REPLYlink written 4.9 years ago by chefarov120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 911 users visited in the last hour