Hi everyone,
I was trying to do the adaptor trimming for my paired end RNA-seq data and I am using trimmomatic. I gave the following commands:
java -jar trimmomatic-0.35.jar PE -phred33 SL264821_1.fastq.gz SL264821_2.fastq.gz SL264821_1_paired.fastaq.gz SL264821_1_unpaired.fastaq.gz SL264821_2_paired.fastaq.gz SL264821_2_unpaired.fastaq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
but it gives me the error Unable to access jarfile trimmomatic-0.35 . Could you please help me with this because I am super new to all of this analysing stuff and kind of lost in this process.
Thank you, Ambika
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2 answers
Is there a file in your current directory named "trimmomatic-0.35.jar"? If not, then you need to provide the full path to that file.
You don't have to make it, you need to download it from the trimmomatic site. If you have already downloaded it, you need to provide the path to that file.
or you can set up a symbolic link
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This is a general error message, indicating that the binary is not found. You sure that the jar is in your current working directory?
No jar is not in my working directory. How can I make one. any suggestions?
You need to download the JAR file to a directory, then move ('cd') to that directory, and from there you can run it.
Please be aware also of full/absolute and relative paths.
In linux, get into the habit of always using full/absolute paths. If you save the JAR file to /home/ambika/Desktop/, then the command would be:
Thank you so much for the explaination, it helped me a lot
No I dont have any files in that directory. So, you mean that I need to provide path to that directory not just the name?