miRDeep2.0.1.2 run showing RNAfold: invalid option -- n

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4.1 years ago

ashenafymamo • 0

I am working on RNA-seq data for studying miRNA from porcine samples. I run miRDeep2.0.1.2 on ubuntu (under the bioconda environment). miRDeep2 took 3 hours to run and gave me the results with an error " RNAfold: invalid option -- n ".

when I look at the results, I got CSV, HTML, and bed formatted results. But the results folder generated by miRDeep2 was empty. The bed file is empty while the other two have results.

Can I take these results or I don't have to take it? any ideas on how to fix this?

RNA-Seq rna-seq • 1.4k views

ADD COMMENT • link updated 4.0 years ago by me.mansoori • 0 • written 4.1 years ago by ashenafymamo • 0

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Please show command lines.

ADD REPLY • link 4.1 years ago by ATpoint 82k

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first run mapper.pl using: mapper.pl reads.fa/1-12h-mockA.fasta -c -i -j -l 18 -m \ -p refdb.fa -s col_1-12h-mockA.fa -t col_V_genom_1-12h-mockA.arf -v

Then I run miRDeep2.pl using: miRDeep2.pl col_1-12h-mockA.fa susScr3.fa col_V_genom_1-12h-mockA.arf ssc_mature_ref.fa mature_other.fa ssc_hairpin_ref.fa none 2>report.log

ADD REPLY • link 4.1 years ago by ashenafymamo • 0

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I have the same problem!

ADD REPLY • link 4.0 years ago by me.mansoori • 0

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Hi,

Same with mine, did you solve it?

Di

ADD REPLY • link 3.9 years ago by di.wang1 • 0

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