How to find/decipher Trimmomatic Output
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5.6 years ago

Hello all,

I have ran this script.

java -jar trimmomatic-0.35.jar PE -phred33 -trimlog /home/richardsonlab/AMMA_transcripts/trimmo30trimlog.txt /home/richardsonlab/AMMA_transcripts/R1V22_B9F8St_ACTTGA_L002_R1_001.fastq /home/richardsonlab/AMMA_transcripts/R1V22_B9F8St_ACTTGA_L002_R2_001.fastq pairedoutput1 unpairedoutput1 pairedoutput2 unpairedoutput2 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:45

I can view the trim log Trimmomatic spit out, however, where can I find my newly trimmed reads? I would like to run them through QC in galaxy. Also, can anyone explain to me what I am looking at in the trim log?

Thanks for your help, Nikelle

trimmomatic QC RNA-Seq rna-seq • 4.8k views
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5.6 years ago
mastal511 ★ 2.1k

The contents of the trimlog file are explained in the Trimmomatic manual,

http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

I don't know where your output files are if you ran this on Galaxy, otherwise they will be in the current directory that you ran Trimmomatic from.

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Thanks Mastal. I have read through the Trimmo Manual previously, it states:

"Specifying a trim log file creates a log of all read trimmings, indicating the following details:

  1. the read name

  2. the surviving sequence length

  3. the location of the first surviving base, aka. the amount trimmed from the start

  4. the location of the last surviving base in the original read

  5. the amount trimmed from the end"

However, looking at my trim log output, I am not sure what corresponds to the 5 items listed above.

DF8F08P1:347:C5YT5ACXX:2:1101:1485:2095 1:N:0:ACTTGA 0 0 0 0 DF8F08P1:347:C5YT5ACXX:2:1101:1485:2095 2:N:0:ACTTGA 0 0 0 0 DF8F08P1:347:C5YT5ACXX:2:1101:1338:2102 1:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1338:2102 2:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1472:2107 1:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1472:2107 2:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1435:2149 1:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1435:2149 2:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1391:2172 1:N:0:ACTTGA 100 0 100 0 DF8F08P1:347:C5YT5ACXX:2:1101:1391:2172 2:N:0:ACTTGA 100 0 100 0

And thank you, I found the files I was looking for; I just can't seem to make sense of the trim log.

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Read name: "DF8F08P1:347:C5YT5ACXX:2:1101:1485:2095 1:N:0:ACTTGA"

"100 0 100 0"

The last 4 space-delimited numbers are the surviving length (100), surviving first base(0), surviving last base(100) and amount trimmed (0) respectively.

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