MiRDeep2_no_inbuilt_reference_genome(whitespace issue with file uploaded)

[nive3437]

Please provide the built-in reference genome, as we are facing an issue with the uploaded reference genome (white space issue) in miRdeep2

[jennaj]

Hi @nive3437

I’m not sure which genome you would like to use but we can definitely (probably?) help to get your reference data interpreted correctly by the tool!

Some examples are in prior topics here. → Search results for 'miRdeep2' - Galaxy Community Help

The short help is to standardize the file formats:

@jennaj

Try cleaning up the fasta file so that just the sequence identifers are on the title lines. You can use the tool NormalizeFasta. Be sure to toggle the option to strip everything after the first white space.

Tools are trying to “match up” the sequence identifiers across different files. So the idea is to isolate the identifiers in each file to make that easier for the tool to process.

So, leave just the sequence identifier in the fasta file > title lines.

Fasta files are best formatted as
>identifier

Not like this (what your first error was complaining about)
>identifier description maybe several words

And not like this (what your second error was about)
>identifier_description_maybe_several_words

The identifier value is what would be in other files:

• BAM, in the @SN lines of the header and the third column of data lines.
• GTF or GFF3, in the third column of data lines
• BED, in the first column of data lines
• More details FAQ: How to use Custom Reference Genomes?

I’m guessing you saw this help already and have a more complicated situation. Would you like to share back the history with the error for troubleshooting? We can craft an exact step-by-step correction for you! → FAQ: Sharing your History

Let’s start there!