Trimmomatic trimming 3' bases

Question

[rob.costa1234]

I want to trim 3' - 20 bases of FASTq in PE file but could not figure out the option @ http://www.usadellab.org/cms/index.php?page=trimmomatic

Any pointer will be highly appreciated.

Thanks

Answer 1

[swbarnes2]

Your question is rather terse, but if you want the last 20 bases gone, it looks like the option you want is CROP.

Answer 2

[shelkmike]

Trimmomatic has no option to trim a fixed number of bases from the 3' end. The option CROP trims the read to a specific length. For example, CROP:20 will make all reads 20 bp long if they were longer than that.

To do what you want, you can use the program Cutadapt with the following command:

cutadapt -u -20 -o reads_trimmed_R1.fastq -p reads_trimmed_R2.fastq reads_initial_R1.fastq reads_initial_R2.fastq