Unable to access jarfile trimmomatic-0.35

Question

[AP]

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

[ATpoint]

This is a general error message, indicating that the binary is not found. You sure that the jar is in your current working directory?

[AP]

No jar is not in my working directory. How can I make one. any suggestions?

[Kevin Blighe]

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:

java -jar /home/ambika/Desktop/trimmomatic-0.35.jar

[AP]

Thank you so much for the explaination, it helped me a lot

[AP]

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?

Answer 1

[Chris Miller]

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.

[AP]

No I dont have any file like that. So I have to make jar file first and then specify the path.

[Chris Miller]

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.

[AP]

Thank you for the information, its really helpful for me.

Answer 2

[kristina.mahan]

or you can set up a symbolic link