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Old 08-25-2011, 10:32 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 08-29-2011, 12:23 AM   #2
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what do you mean by aligning expression ? the reads ?
NicoBxl is offline   Reply With Quote
Old 08-29-2011, 05:44 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 06-24-2016, 12:04 AM   #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, 10:12 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
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Old 09-29-2017, 03:29 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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