Hi all,

I am analyzing my RNA-seq data using Trinity pipelines. My libraries were prepared from different tissues of different gender (plants). I used my libraries from all types of tissues of the female for de-novo assembly and use males' ones for a separate assembly. Once two separate assemblies were created, I used CD-HIT to combine two transcriptome assemblies to make a representative reference transcriptome file so I can use for DEG downstream analyses. Here's my question, I am wondering how they are some genes have "0" counts in all of libraries regardless tissue types or genders, it's just "0" across the libraries. The reference transcriptome file was based on the libraries but they libraries do not have those gene expression. I do not understand how this could happen. Would you kindly explain what happens? Thanks,