Error in running miRDeep2
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Entering edit mode
6 weeks ago
DEEPESH • 0

Hi I am trying to run miRDeep2 for identification of miRNAs.

But its showing error miRNA reference this species file mature_osa.fa has not allowed whitespaces in its first identifier.

I checked it properly and matched with the file given in miRDeep2.pl tutorial, my file is also has a same pattern. I used sed command also but issue is not resolved

Whitespace miRDeep2 error • 188 views
1
Entering edit mode
29 days ago
Paolo ▴ 10

I found the same problem. I understand that I can test my input for errors with:

sanity_check_mature_ref.pl bta_mature.fa


This is the error I got:

Error in line 1: The identifier

bta-miR-26a MIMAT0003516 Bos taurus miR-26a

contains white spaces

I.  Sequences are allowed only to comprise characters [ACGTNacgtn].
II. Identifiers are not allowed to have withespaces.

You could run remove_white_space_in_id.pl inputfile > newfile
This will remove everything from the id line after the first whitespace


So by calling

remove_white_space_in_id.pl bta_mature.fa > bta_mature.fa.fix


I was able to run mirdeep2 without problems

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Entering edit mode

Thank you.

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Entering edit mode

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