I tried to run cutadapt in the terminal, but I always keep getting the same error.
I tried to use trim_galore on my data, but same thing happened. I keep getting an error message saying "Illegal division by zero" or something along the line of that. I eventually found out that I need cutadapt, but I can't even get cutadapt to work.
I asked someone higher up for help and I was told to just make a python script because it would be easier to remove the adapter sequences than trying to get the software to work.
My questions:
1. How come cutadapt and trim_galore are impossible for me to run on linux terminal?
2. What is some other software that I could try? I am trying to clean the data for 2 paired end fastq files after looking at the FASTQC reports.
I just don't know how I am supposed to come up with a python script that removes adapter sequences when I don't even know what an adapter sequence is.
I'm pretty much lost and I don't know how to get past the "cleaning stage". I'm sure it will get much more difficult during the "mapping stage" and the "analysis stage", but honestly I am completely lost.
It's very difficult to keep going at it when the software I'm supposed to use doesn't even work.
I tried to use trim_galore on my data, but same thing happened. I keep getting an error message saying "Illegal division by zero" or something along the line of that. I eventually found out that I need cutadapt, but I can't even get cutadapt to work.
I asked someone higher up for help and I was told to just make a python script because it would be easier to remove the adapter sequences than trying to get the software to work.
My questions:
1. How come cutadapt and trim_galore are impossible for me to run on linux terminal?
2. What is some other software that I could try? I am trying to clean the data for 2 paired end fastq files after looking at the FASTQC reports.
I just don't know how I am supposed to come up with a python script that removes adapter sequences when I don't even know what an adapter sequence is.
I'm pretty much lost and I don't know how to get past the "cleaning stage". I'm sure it will get much more difficult during the "mapping stage" and the "analysis stage", but honestly I am completely lost.
It's very difficult to keep going at it when the software I'm supposed to use doesn't even work.
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