Hi everyone!
I am a Biology undergrad and I use bioinformatics for my Bachelor thesis. I'm still learning so be nice to me. There is something wrong with my command for trimmomatic, it executes, but the resulting file has two problems: it is too large and its name is followed by LEADIN:25, which is part of the command, like this: output.fastq.gzLEADIN:25. This is the command I use:
This is the output:
It looks like the LEADIN:25 part is not working, that's why the output file is too large, even larger than the input file. So I think there must be some separation between the output and the LEADIN:25 in the command but I don't know how to put it.
Can you tell me what is wrong?
Thank you!
I am a Biology undergrad and I use bioinformatics for my Bachelor thesis. I'm still learning so be nice to me. There is something wrong with my command for trimmomatic, it executes, but the resulting file has two problems: it is too large and its name is followed by LEADIN:25, which is part of the command, like this: output.fastq.gzLEADIN:25. This is the command I use:
Code:
java -jar $trimmomatic SE input.fastq.gz output.fastq.gz LEADIN:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:25
Code:
TrimmomaticSE: Started with arguments: input.fastq.gz output.fastq.gzLEADIN:25 TRAILING:25 SLIDINGWINDOW:4:20 MINLEN:25 Automatically using 1 threads Quality encoding detected as phred33 Input Reads: 33081999 Surviving: 20602256 (62,28%) Dropped: 12479743 (37,72%) TrimmomaticSE: Completed successfully
Can you tell me what is wrong?
Thank you!