Want to trim off last 50 bases from 151 bases read using trimmomatic?

Question

[bioinforesearchquestions]

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

[GenoMax]

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

[bioinforesearchquestions]

Thanks for providing me the command.

Answer 1

[igor]

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

[bioinforesearchquestions]

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?

[igor]

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