Question: SOAPdenovo trans min contig issue
gravatar for Biogeek
3.2 years ago by
Biogeek380 wrote:

Hey guys,

I'm running soapdenovo TRANS and I am trying to give a cut-off contig length of minimum 200, rather than the 100 default using the -L flag.

./SOAPdenovo-Trans-127mer all -s config_file -o K91 -K 91 -L 200 -p 30

My output file .scafStatistics, still reports (sequences/scaffolds above 100bp). Why is the -L flag not working, should I be using some other flag?

Additionally, is it normal to keep gaps put out in the scafSeq file or do people close them in transcriptome assemblies?


denovo soap help • 1.1k views
ADD COMMENTlink written 3.2 years ago by Biogeek380

I have faced with the same problem about the min contig length. After running, you can remove all contigs less than 200 bp from the final assembly. Regarding gap, I used a software (sorry, don't remember its name), but its results weren't fantastic.

ADD REPLYlink written 3.2 years ago by seta1.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1987 users visited in the last hour