miRDeep2- mapper problem with perl install.pl installation?
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.
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The error message is telling you the two command you need to run.
Hi, I have run this perl command in mirdeep2_pa folder many times but still it is giving error.
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:
Have you tried to run
mapper.plafter 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 likecontrol1.fastqorreads_collapsed.fa.