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:

~/trinityrnaseq_r2012-01-25/Trinity.pl --kmer_method meryl \
--seqType fq --single SRR057742.fastq --CPU 1

>comp1_c0_seq1 len=206 path=[1:0-205]
AAGCAGAAGACGGCATACGACCAAGGCCTCTAGTCATTCGCTTTACCGGATAAAACTGCT
CAGCGAGCGCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGA
TTAGTCTTTCGCCCCTATACCCAGGTCGGACGACCGATTTGCACGTCAGGACCGCTGCGG
GCCTCCACCAGAGTTTCCCCTGGCTT

Any ideas what I can try?

asked 21 May '12, 16:58

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Customer
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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.

(21 May '12, 16:58) SupportRep

Try Edena if you are working with prokaryots

link

answered 21 May '12, 16:58

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SupportRep
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Asked: 21 May '12, 16:58

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Last updated: 21 May '12, 16:58

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