Entering edit mode
7.7 years ago
Biogeek
▴
470
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.
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.