How to find/decipher Trimmomatic Output

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 rna-seq qc

• 9,078 views • link

updated 2.4 years ago by Ram

• written 10.4 years ago by nikelle.petrillo

1 answer

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.

• 1 views • link

written 10.4 years ago by mastal511

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:

the read name
the surviving sequence length
the location of the first surviving base, aka. the amount trimmed from the start
the location of the last surviving base in the original read
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.

• 1 views • link

written 10.4 years ago by nikelle.petrillo

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.

• 0 views • link

written 9.4 years ago by Dchoy •