Question: Want to trim off last 50 bases from 151 bases read using trimmomatic?
0
gravatar for bioinforesearchquestions
2.9 years ago by
United States
bioinforesearchquestions200 wrote:

Hi All,

I have raw paired-end fastqc files of read length (151 bases). I would like to trim off last 50 bases and would like to keep just 101 bases from each read. I used following command to perform the activity. Am I missing something or good to go?

Currently the program is running, I couldn't see the output. But I would like to about the parameters I have used.

java -jar trimmomatic-0.32.jar -threads 6 PE -phred33

S1_L001-L004_R1.all.fastq.gz S1_L001-L004_R2.all.fastq.gz

S1_L001-L004_R1.all.paired.trimmed.fastq.gz

S1_L001-L004_R1.all.unpaired.trimmed.fastq.gz

S1_L001-L004_R2.all.paired.trimmed.fastq.gz

S1_L001-L004_R2.all.unpaired.trimmed.fastq.gz

ILLUMINACLIP:Trimmomatic-0.32/adapters/Illumina-TruSeqAdapter.fa:2:30:10

ILLUMINACLIP:Trimmomatic-0.32/adapters/Illumina-MultiplexingPrimer.fa:2:30:10

CROP:101

LEADING:20

TRAILING:20

MINLEN:20

rnaseq fastq dnaseq trimmomatic • 1.4k views
ADD COMMENTlink modified 2.9 years ago by igor7.6k • written 2.9 years ago by bioinforesearchquestions200

You should be able to look at the result file while the program is running (zmore or gzip -c filename | more).

ADD REPLYlink written 2.9 years ago by genomax65k

Thanks for providing me the command.

ADD REPLYlink written 2.9 years ago by bioinforesearchquestions200
1
gravatar for igor
2.9 years ago by
igor7.6k
United States
igor7.6k wrote:

Do you need to use Trimmomatic?

If not, then I would suggest fastx_trimmer from FASTX-Toolkit, which would be quicker and easier: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_trimmer_usage

ADD COMMENTlink written 2.9 years ago by igor7.6k

Hi Igor,

Thanks for suggesting me the fastx_trimmer. The reason why I chosen trimmomatic is, it has list of adapters and primers in fasta format. But in fastx_trimmer I will be able to provide only a single string of adapter.

$ fastx_clipper -h usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]

Does it looks reasonable, if I use fast_trimmer to trim last 50 bases and then use that trimmed fastq file to trimmomatic to do the quality trimming and adapter trimming?

ADD REPLYlink written 2.9 years ago by bioinforesearchquestions200

Sounds reasonable to me. Although if you have to go back to Trimmomatic anyway, it may be a little wasteful.

ADD REPLYlink written 2.9 years ago by igor7.6k
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