I am try to do de-novo assembly from my RNA-seq data.. first program which I used was SoapDeNovo-Trans and it works very well and there is provide some very good statistic information about scaffold and contigs..
Right now I am try to de-novo assembly with Trinity. My output is in FASTA file and does Trinity do scaffolding? I can find just information about contig N10-50 and number of transcripts and genes..
I would like to compare result form SoapDenovo-Trans and Trinity, but not sure how to get scaffold information from trinity output..
Or if you have any other experiences how to compare output from different programs please share it with me..
Many thanks for any help..