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Old 10-17-2011, 05:09 AM   #1
victoryhe
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Default noncoding RNAs

Hi,

how can i get how many transcripts map to rRNA genes, tRNA, snoRNA, microRNA, lincs ,etc, respectively? manually do i count them? is there any tool or package to do it?

any tips would be appreciated,
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Old 10-17-2011, 05:16 AM   #2
NicoBxl
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align your reads against the rfam and mirbase databases
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Old 10-17-2011, 10:29 AM   #3
heytreeful
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if you're dealing with small RNA seq, mirTools and DSAP are two online pipelines that automatically do the alignment for you (mirTools is better I think). You can see if it accepts longer reads.
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Old 10-17-2011, 11:30 AM   #4
victoryhe
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not small RNA, i am taking a look at RNA-Seq data. for this, rFAM is better, right? anything else?
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