Experience with SOAP trans
Hey guys,
some quick questions. New to SOAPtrans de novo assembler.
q1. Given that the output of trinity is a .fasta file, the file that I use from SOAPtrans for downstream analysis is the .scafSeq file?
q2.For de novo assembly, what is the consensus for scaffold gap filling. Do people use the -F option normally, or is it normal to leave the scaffolds with gaps?
Thanks.
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Anyone can provide some detail?
Your end goal dictates whether you want to use the contigs or scaffolds files.Default value for -F is 'NO', but again, what is your end goal?
If you're new to de novo transcriptome assembly, Trinity may be easier for you to use.