Hi,
I've been playing with Galaxy lately to do my data analysis for smallRNA (Illumina).
I think I'm getting what I want but I'm stuck at a certain point.
Here are the tools/workflow I have used:
1. FastQC (to check quality)
2. Clip (to trim off 3' adapter sequence)
3. Sickle (to discard any bad quality sequences)
4. MiRDeep2 mapper to collapse the reads from Sickle (seems to just make the sickle file compatible with MiRDeep2 Quantifier)
5. MiRDeep 2 Quantifier to map the collapsed reads to the reference fasta file of mature miRNA.
*Result is a list of miRNA in a tabular format
-Next I want to convert this file to a file compatible with edgeR for differential expression analysis. Any thoughts on how to do this? Any known tools?
-Also, there is one other tool: MiRDeep2 (identification of novel and known miRNAs). I can't for the life of me figure out if this tool is more useful or if I should be using this one instead of Quantifier however the output when I use this tool is not giving me the miRNA list I would expect. Any help would be appreciated. Thx!!
I've been playing with Galaxy lately to do my data analysis for smallRNA (Illumina).
I think I'm getting what I want but I'm stuck at a certain point.
Here are the tools/workflow I have used:
1. FastQC (to check quality)
2. Clip (to trim off 3' adapter sequence)
3. Sickle (to discard any bad quality sequences)
4. MiRDeep2 mapper to collapse the reads from Sickle (seems to just make the sickle file compatible with MiRDeep2 Quantifier)
5. MiRDeep 2 Quantifier to map the collapsed reads to the reference fasta file of mature miRNA.
*Result is a list of miRNA in a tabular format
-Next I want to convert this file to a file compatible with edgeR for differential expression analysis. Any thoughts on how to do this? Any known tools?
-Also, there is one other tool: MiRDeep2 (identification of novel and known miRNAs). I can't for the life of me figure out if this tool is more useful or if I should be using this one instead of Quantifier however the output when I use this tool is not giving me the miRNA list I would expect. Any help would be appreciated. Thx!!
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