Zero coverage regions from mapping back reads to the transcriptome assembly

Question

[seta]

Hi all,

I've recently got the reads from the RNA sequencing of one sample on the one lane of Illumina Hiseq2000. After making transcriptome assembly and mapping read back to the assembly, I found that the average coverage is about 400, and there are about 15000 contigs with zero coverage. My question is: if can I remove the contigs with zero coverage from the initial assembly before annotation step and blast, it sounds reasonable? please let me know what you know about it.

Thanks in advance