Trimmomatic trimming 3' bases
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
• 2,057 views
•
link
2 answers
Your question is rather terse, but if you want the last 20 bases gone, it looks like the option you want is CROP.
• 0 views
•
link
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
• 0 views
•
link
Log in to answer this question.