miRdeep 2 quantifier

usegalaxy.org support
1

I am trying to run the second step of quantification (i.e. quantifier) following the mapper module of mirDeep2. In the mapping step everything is fine and I get the collapsed reads to be given to the quantifier module. Then, when trying to run the quantifier module, providing mature, precursor and star sequences, the run ends with an error which apparently lacks any suggestions on where the error is.

Here a screenshot of my files

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Do I have to index these files in bowtie?
I hope you can help me

2

Hi @Sabrina_Napoletano

Would you please share the data within the context of your Galaxy history? That will capture details of the run that will usually matter when troubleshooting. Meaning: the data, server, tool/version, parameters, command-string, logs. All of the related details about how all of those inputs were consumed by the tool at runtime with context leads to the best actionable help.

How-to: Troubleshooting errors

3

Hi jennaj thank you for your reply, this is the output of my run

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image1920×1020 134 KB

these are the strings of the files I used for the history
reads.fa
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hairpin.fa
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image1920×1020 53 KB

mature.fa
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image1035×549 81.8 KB

4

Your example doesn’t look like an error. Am I misunderstanding?

5

Hi, thank you for your reply, in other blogs I read that it could be

there were mismatches between fasta identifiers in the provided miRNAs (precursors, star and mature)

However they don’t suggest how solve this problem

Do you have any suggestion?

Thank you very much

6

Hi @Sabrina_Napoletano

You could still share your history, and we’ll help with a more detailed review.