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Old 08-25-2011, 09:32 AM   #1
Location: Maryland

Join Date: Jun 2011
Posts: 16
Default miRDeep2


I Am currently using miRDeep to to analyze small RNA-seq data from the Solid 4.

However I am having trouble aligning expression between samples.

Does anyone have experience with miRDeep that could suggest a method or suggest another mapping/analysis program.


asaleh is offline   Reply With Quote
Old 08-28-2011, 11:23 PM   #2
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what do you mean by aligning expression ? the reads ?
NicoBxl is offline   Reply With Quote
Old 08-29-2011, 04:44 AM   #3
Location: Maryland

Join Date: Jun 2011
Posts: 16

sorry I was not more clear.

I mean aligning the reads for each microRNA from different samples. The output does not lend itself to that as far as I can figure out. Just wondering if others had encountered this problem and figured out how to solve it.
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Old 06-23-2016, 11:04 PM   #4
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I am trying to identify miRNA from fastq file. I am using miRDeep2 for this purpose. As mentioned in the in the tutorial regarding the mature and precursor sequences of miRNA, I have downloaded it from miRBase version 21. While running the command im getting this error in the report.log file.

" #Starting miRDeep2 /home/titan4/mirdeep2_0_0_8/src/ reads_collapsed.fa hg38.fa reads_collapsed_vs_genome.arf mature_new.fa none precursor_new.fa -t H.sapiens

miRDeep2 started at 12:3:54

mkdir mirdeep_runs/run_24_06_2016_t_12_03_54
testing input files

started: 12:3:54 mature_new.fa

Error: problem with mature_new.fa Error in line 5.177: The sequence

contains characters others than [acgtunACGTUN]

Please check your file for the following issues:

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

Can some one help.
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Old 12-09-2016, 09:12 AM   #5
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Location: indiana

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It looks like you likely have whitespaces in the headers of your fasta file, which mirDeep does not allow. See for various options on how to remove these
natallah is offline   Reply With Quote
Old 09-29-2017, 02:29 AM   #6
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Location: india

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Default Novel MicroRNA prediction with Mirdeep 2.

I recently done small RNA sequencing of my endocrine tumour samples. I got result analysis with Mirdeep2 . I am not master in bioinformatics so , i outsourced the analysis. The company have predicted some novel micrornas. They have used mirdeep2 software for predicting novel microRNA.

I am facing problem in selecting novel microRNAs from small RNA sequencing. Is it necessary to have high mirdeep2 score with high mature read count. Those sequence with high mirdeep2 score ( like 3168) & mature read count (456) have non significant RANDFOLD p value. I am confused in this part.

I read in mirdeep2 documentation in which the score cut was from -10 to 10.but i am getting mirdeep2 score of like 200 , 361. I am really very confused. Then i started comparing total read length , loop read length. But still confused.

Please guide me regarding mirdeep2 software and please help me its parameters for selecting novel microRNA.I will be very thankful to you.
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