I'm new to Trimmomatic and am having trouble producing the 4 output files from a PE trim. I am running Trimmomatic 0.32 in OSX. When I issue the following command in terminal:
jlg:~ jgregg$ java -jar /Applications/Trimmomatic/Trimmomatic-0.32/trimmomatic-0.32.jar PE -threads 2 -phred33 -trimlog /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/TrimLog235 /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Test_R1.fq.gz /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Test_R2.fq.gz -baseout /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/TestOUT_IA235.fq.gz ILLUMINACLIP: /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Trimmo_IA235.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:37
This runs for a few minutes and then I get:
Input Read Pairs: 17222594 Both Surviving: 13577333 (78.83%) Forward Only Surviving: 3273911 (19.01%) Reverse Only Surviving: 149140 (0.87%) Dropped: 222210 (1.29%)
This looks right, but the only files that are produced are the TrimLog file, and two files (TestOUT_IA235.fq.gz and Trimmo_IA235.fa/2/30/10) that contain sequences that have adapters. These appear to be the half of the sequence pairs that should have been discareded. Any help that people can offer would be greatly appreciated.
Jake
jlg:~ jgregg$ java -jar /Applications/Trimmomatic/Trimmomatic-0.32/trimmomatic-0.32.jar PE -threads 2 -phred33 -trimlog /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/TrimLog235 /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Test_R1.fq.gz /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Test_R2.fq.gz -baseout /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/TestOUT_IA235.fq.gz ILLUMINACLIP: /Users/jgregg/Documents/ICH_Genomics/IchPE76/PE76_filtered_reads/Process_Testing/Trimmo_IA235.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:37
This runs for a few minutes and then I get:
Input Read Pairs: 17222594 Both Surviving: 13577333 (78.83%) Forward Only Surviving: 3273911 (19.01%) Reverse Only Surviving: 149140 (0.87%) Dropped: 222210 (1.29%)
This looks right, but the only files that are produced are the TrimLog file, and two files (TestOUT_IA235.fq.gz and Trimmo_IA235.fa/2/30/10) that contain sequences that have adapters. These appear to be the half of the sequence pairs that should have been discareded. Any help that people can offer would be greatly appreciated.
Jake
Comment