Trim 100bp PE sequencing to 50bp reads

Question

[Jautis]

Hello, we're doing some QC for future sequencing and want to have an empirical comparison of 100bp SE reads with 50bp PE reads. Starting with 100bp PE reads, how can I trim the fastq file to the first 50 bases? (i.e. retain the first 50 characters for each even-number row). Thanks!

Answer 1

[GenoMax]

Using reformat.sh from BBMap suite:

reformat.sh -Xmx4g in1=R1.fq.gz in2=R2.fq.gz out1=trim_R1.fq.gz out2=trim_R2.fq.gz forcetrimright=50

seqtk (LINK) by Heng Li:

seqtk trimfq -e 50 R1.fq > R1_trim.fq

Answer 2

[cpad0112]

$ cutadapt -l 50 -o out1.fq -p out2.fq input_R1.fastq input_R2.fastq
$ cutadapt -l 50 -o out1.fq  input_R1.fastq 

if SE fastq headers are not 50 characters long, you can try this: colrm 51 < test_R1.fastq > out_R1.fastq. colrm is available most of the *buntu distros.