Mirdeep not giving results.

Question

[A. Blue]

I'm trying to find novel miRNA involved in cardiovascular diseases. I tried with both RNA samples and miRNA samples. I ran about 14 samples to no avail. Once or twice a result file got saved but I'm unable to open it. What might be going wrong or what can I do to get results. Any help is appreciated!!

PS: it's mirdeep software not mirdeep2.

[Michael]

It is hard to analyze the problem at hand without more information, in particular, program versions, command calls and exact error messages and run logs. It is hard to believe that a program run would produce no output or files at all, most likely the necessary keys are in that output. There is a slight possibility that no novel miRNAs could be detected because the human miRN'ome is well covered already, but it is way too early in the debugging process. Any specific reasons for not using mirdeep2?

[A. Blue]

It's not even showing the known list of miRNA in the sample. Let alone novel. I'm just running raw samples from sra after bowtie.

I'm using sra sequences, so I'm unable to find the adaptor list for the respective sequence. I had run a sample once in mirdeep2 of the galaxy server but it showed error in the output.

[Michael]

The level of detail is still way too low. So you are running this in galaxy? Please provide more information or we cannot help you, including but not limited to:

• operating system or environment (Linux, galaxy,...)
• versions of all programs involved
• the exact command call (copy pasted as text)
• the complete console output during a run (copy pasted as text, no screen shots)
• example of the SRA id of your download
• any log output that could be helpful