detect lncRNA by clc
Hi everybody, I want detect lncRNA from some human (control and treatment) RNA-seq data ( Illumina sequencing data) in fastq format, I detect genes and get Differential Expression by CLC genomics software, but I don’t know how I can get Differential Expression lncRNA by CLC genomics? I saw In two articles, de novo assembly pathway and discovery detection pathway was used, I tried them separately but I do not know how to use the results of these pathways. Also,Is it true finds lncRNA from same RNA-seq data that I use for detecting genes or I should find only RNA - seq of non-coding RNA? Your attention would be really appreciated.
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Two recent papers that appear to have used CLC for this purpose.
http://www.nature.com/articles/srep22698
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585956/
If you are interested in using CLC, it would be really good if you contact CLC support because most of the people here work on open source softwares and its very less likely that we know about CLC.