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What are the recommended tools for de novo assembly of Illumina sequencing of small RNAs (like miRNAs, snoRNAs, etc) of a read length of 36bp for a eukaryote multicellular species without a reference genome? I tried the latest version of Trinity with default parameters on the public dataset from the SRA: http://www.ncbi.nlm.nih.gov/sra?term=SRR057742 And it only gives me 1 transcript back:
Any ideas what I can try? |
it depends on how the libraire is prepared. In general, with small RNA sequencing, the librairie is enriched in miRNA and other small ncRNA. So the lib is not mRNA enriched.