SOAPdenovo trans min contig issue
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?
Thanks.
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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.