ncRNA analysis of a Leukemia assembled transcriptome

[Giorgio C]

Hello,

i'v assembled with Newmbler a transcriptome of Leukemia.
I have put all my singleton , ncrna sequences, " no Hits" coming out from blast (hg19) in "mirTool" to verify and classify this sequences.
mirTool give me a file with 100% of unclussified and no miRNA, no tRNA , no snRNA found. How is possible this result? I have more than 20.000 sequences, it's so strange. Do you know any software toll to analyze this data that i find difficult to annotate? Particularly i am interested to have a table for the ncRNA (% of tRNA, % of miRNA, ....)


Thank you very much

[Giorgio C]

Nobody has an anwer for me? Please anything may be helpuful

[zukey]

Our internal software may help....

Length of your sequences? Which sequencing platform, illumina or 454?
We have a internal-built program ACGT101 to analysis the miRNAs including filtering tRNAs from RFam database. If you need our help, please email the raw data link to me [email protected]. I can try your data with this miRNA analysis program. Free. :-)

Thanks,

Qi

[Giorgio C]

Thank you for your answer,
I'd like to analyze the singleton file ( 20-120 nt) and another file with "long ncRNa" (100-600 nt). I'm a 454 user, Do you think is possible help with your program ?

[zukey]

Could you send me the link to short reads or part of them? I will give a try.

Thanks,

Qi

[ppgardne]

Probably best to use tRNAscan-SE for tRNA annotation rather than Rfam.

[Giorgio C]

Hello, here you can find the file: http://www.mediafire.com/?qi47nsw8zb7jqhv
I wait for your instructions
Thank you very much

[odelfour]

Hi Giorgio,
Maybe you can have a look at DSAP: http://www.ncbi.nlm.nih.gov/pubmed/20478825
DSAP is available at http://dsap.cgu.edu.tw

Olivier

[Giorgio C]

Thank you very much Olivier !!!

[yjhua2110]

You can look at deepBase: http://deepbase.sysu.edu.cn/, a platform for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, snoRNAs...) from deep sequencing data.

You also can use snoSeeker (http://genelab.sysu.edu.cn/snoSeeker/) for snoRNA discovery and annotation from deep sequencing data.