I am having a problem getting trimmomatic to find the adapter file. I have tried all the options I can think of for the path, and put the file in the trimmomatic folder but still get a file not found error message. I can't spot any syntax errors, so can anyone help me?
error: java.io.FileNotFoundException: /adapters/Truseq3-PE-2.fa (No such file or directory)
java -jar trimmomatic-0.36.jar PE -phred33 27_4_24_LC_R1.fq 27_4_24_LC_R2.fq 27_4_24_LC_forward_paired.fq 27_4_24_LC_forward_unpaired.fq 27_4_24_LC_reverse_paired.fq 27_4_24_LC_reverse_unpaired.fq ILLUMINACLIP:/adapters/Truseq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Thanks
error: java.io.FileNotFoundException: /adapters/Truseq3-PE-2.fa (No such file or directory)
java -jar trimmomatic-0.36.jar PE -phred33 27_4_24_LC_R1.fq 27_4_24_LC_R2.fq 27_4_24_LC_forward_paired.fq 27_4_24_LC_forward_unpaired.fq 27_4_24_LC_reverse_paired.fq 27_4_24_LC_reverse_unpaired.fq ILLUMINACLIP:/adapters/Truseq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Thanks
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