Question: miRDeep2- mapper problem with perl install.pl installation?
0
gravatar for harshraje19
10 months ago by
harshraje1930
harshraje1930 wrote:

Dear all, Happy new year 2020.

I am performing the small RNA seq data analysis and I want to find the miRNAs in my data using the miRDeep2.

I have indexed my genome successfully using the command bowtie-build genome.fa genome

But when I run the command

mapper.pl control1.fastq -c -j -l 18 -m -p genome \ -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v

for mapping it always fail and instructs me to run the perl install.pl script in miRDeep package folder. Then I run this script in miRDeep package but problem remains same.

Following is my error message on terminal.

harshraj@harshraj-XPS-8930:~/Desktop/SmallRNAseqdata$ mapper.pl control1.fastq -c -j -l 18 -m -p genome \ -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v

Please run the install.pl script first before using the miRDeep2 package
The install script is located in /home/harshraj/mirdeep2_pa so just do

cd /home/harshraj/mirdeep2_pa
perl install.pl

What should I do in this case? Can anyone help me out

Thank you in advance.

ADD COMMENTlink modified 10 months ago • written 10 months ago by harshraje1930

The error message is telling you the two command you need to run.

$ cd /home/harshraj/mirdeep2_pa
$ perl install.pl
ADD REPLYlink modified 10 months ago • written 10 months ago by genomax92k

Hi, I have run this perl command in mirdeep2_pa folder many times but still it is giving error.

ADD REPLYlink written 10 months ago by harshraje1930

From the code you have given it seems that you try to run a script in a wrong folder: ~/Desktop/SmallRNAseqdata. What is the output on terminal after you run these commands:

$ cd /home/harshraj/mirdeep2_pa
$ perl install.pl

Have you tried to run mapper.pl after these 2 commands? In case that your files are in ~/Desktop/SmallRNAseqdata folder and the script is in /home/harshraj/mirdeep2_pa folder you will have to adjust paths to data files like control1.fastq or reads_collapsed.fa.

ADD REPLYlink modified 10 months ago • written 10 months ago by zubenel110
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