TRIMMOMATIC ERROR ON WINDOWS/CYGWIN

Question

[Beyza]

Hi everyone, I am trying to install Trimmomatic and use it to RNA-seq in my Windows computer. But unfortunately, there is an error that I can't fix. Could you please help me ? Thanks

[GenoMax]

Please consider this answer before you spend a lot of time with cygwin : Install trimmomatic on windows computer?

You should consider using Windows subsystem for Linux instead, if you are using Windows 10 or 11.

Answer 1

[Pierre Lindenbaum]

minimal command line for trimmomatic needs output for paired and unpaired fastsq: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

java -jar trimmomatic-0.30.jar PE s_1_1_sequence.txt.gz s_1_2_sequence.txt.gz
lane1_forward_paired.fq.gz lane1_forward_unpaired.fq.gz lane1_reverse_paired.fq.gz
lane1_reverse_unpaired.fq ....
`

where are your output path ? paired and unpaired ?