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Sorry if this has been asked before, I've done a quick search and I don't think there's an easy explanation for me to understand.

I'm really new to bioinformatics/RNASEQ analysis, having only taken up an attempt to process my RNASEQ data last week. I have 0 background and some rudimentary knowledge of command line. So far I've managed to get access to my universities HPC and perform a fastqc on my fastq data.

What I'm stuck at at the moment is attempting to trim my RNASEQ data and remove adapters. My data had been run through Novaseq and I'm not exactly sure how to trim my current RNASEQ data.

I've attempted to run the following script using trimmomatic

# go to working folder
cd /project/CHR_RNASEQ/reads

# run trimmomatic
trimmomatic SE -threads 8 -phred33 SLIDINGWINDOW:4:20 ILLUMINACLIP:$TRIM/adapters/TruSeq3-SE-2.fa:2:30:10 MINLEN:36 1_R1.fastq.gz 1_R1_trimmed.fastq.gz

It did log a job in the HPC, but I had no output at the end. I didn't receive an error either. This is unfortunately just some code I had lifted and trialed and errored until something finally ran, but I'm very sure I'm very wrong and any help with understanding this would be really appreciated.

Cheers

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  • $\begingroup$ If you're using a HPC please talk with your IT department to check which job scheduler they are using: LSF, SGE, SGE, SLURM, PBS. Most of cases you are not able to run any job without this queue system. $\endgroup$
    – zorbax
    Mar 4, 2020 at 15:21

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Depending on the cluster management tool, you might have received e-mails when the "job" begins and ends. If so, you can check the "Exit status" of the job. For example, in the case of our HPC the relevant lines from the "job completion e-mail" would be:

Execution terminated
Exit_status=0

BTW, at first I was confused with the phrase "Execution terminated", however, in the scheduler used in our system, it means "the run has been successfully or unsuccessfully completed". Exit_status=0 int the next line means a successful run and for the unsuccessful runs there is a list with the error codes.

Secondly, if your run was successful, you would see new fastq files containing "_trimmed" in the filename (reading this from your code). These fastqs should be more or less similar in size to the original depending on how aggressive the trimming settings are.

If you can provide more information, i.e. the type of cluster management tool used, the log file, ..., you can get more help and precise answers from the community.

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  • $\begingroup$ okay, I'm really sorry, but I'm not sure what you mean by cluster management tool or log file. I tried looking around for information on this, and did get kind of stuck. I looked in the HPC for my file, and couldn't find one, so i'm assuming it ran the job but didn't actually give me an output. $\endgroup$
    – user7322
    Mar 3, 2020 at 6:50
  • $\begingroup$ You wrote "It did log a job in the HPC", what is in this? In my case, there are two logs at the folder from which I submit my job, one like "jobname.ejobid" and the other "jobname.ojobid". The first is the error log and the second for the output from the software you are running. Do you have these? $\endgroup$
    – haci
    Mar 3, 2020 at 7:16

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