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?