We have raw data in COLOR space format (.csfasta) and would like to profile and analyze it in order to find known and novel miRNA in sample. Further we are also looking for different expression between two samples.
Any suggestion?
Actually I am facing problem to handle directly from .csfasta because as per my survey, I know many tools (web services/offline tool ) but No one or very few able to handle .csfasta file for analysis of mapping, known, novel and different experience.
You can try TopHat but with use of bowtie not bowtie2 (--bowtie1 switch).
If you allign to tthe ranscriptome I would recomend SHRiMP2 and then BitSeq (http://bioinformatics.oxfordjournals.org/content/28/13/1721.short).
An option should also be Subread (http://nar.oxfordjournals.org/content/early/2013/04/03/nar.gkt214.full.pdf+html)
Dear sir,
I have only small RNA reads instead of whole transcripts. So could you suggest me tools for particular miRNA profiling ???
Thanks in advance..
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- Biological Science
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- microRNA