option for filling gaps in scaffolds

[Liyong-Zhang]

Hello there,

I am using SOAPdenovo-Trans to assemble a transcriptome. After it finished, I notice there are strings of 'N' introduced in the transcripts. e.g.
>scaffold1 Locus_0_0 81.6 COMPLEX
CTGGAGTTGTTGGAAACGTTGAGGTGACTTTGAAACGGATCAGAACAGCCTTTTTTGTTTTCTTTATCTTAGATCGATCTATTAAATTCAAGTATGTGTTTGATATTTGGTGCAGAGACAACTTGGAAAATGGGATTTCTTAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGGTGGATGAAAGAAGCATTAGATGTTTTGGTTGAGAGACTCTCATCACCAATGAATCAACCAAAGGAAGAGAAGACTATCTCTATCTCTATTGAGACAATGTGCTGATGAAGTCATCCATGATTGCTACAATTGCTGATTTGCGATGGGGAGTTTTTATAAACTAATGGATCCTCTGTAGGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTTCAGGCCAAAGCTCAAGTTGTTCTGTAACAAGCATAGGGAACATTAGCCCTTCATAGTATGTTCCTCTGCTTTTGCTTAAAAAATCCCATTTTCCAAGTTGATGCTCAATGTTGCCAAGAACTCCAGCTTCTTCACGACATTCTCTTGAAGCAGCTTCTTCTACAGATTCATCAAGCTCCCAACCACCCTTNNNNNNNNNNNNNNNNAACCCTTCGAATCTCTATGGTCGGTTTAGTTTTTGTTTCTGCTTTTTAAGTGTTTATGATTCGATTCGTTACGCCTGAAAAGATTTGATTTGTGAGAGAGAGAGATGGGAGAAGAAGAAGAAGAAGANNNNNNNNNNNNNNNNNNNNNNNNNNTATCCGTTATAGTTGTTACACTCATCTTTCCTCTTTTTGTTCTTTATAAAATCATCCTCCTTGCTTCTTTATTATTCTGGCCAAAACAAGATTTAGGGTTCT

After google around, I found tool SOAPdenovo2-GapCloser to fill the gaps. Also, I realize SOAPdenovo-Trans has a parameter -F (optional) fill gaps in scaffolds, [NO].

I guess I could use GapCloser to fill the gaps for current assembly, or re-run SOAPdenovo-Trans with -F. My question is whether these two result transcriptomes will be any different? If so, which strategy should I go with to get better result?

Many thanks!