How to use trimmomatic to cut the final part of bases

Question

[users2023]

HOW CAN I USE trimmomatic a flexible read trimming tool for illumina ngs data for base sequnce content FOR CUT THEN FINAL PART OF BASES

[GenoMax]

Please be patient. People answering on the site are volunteering their time for free. Don't post similar content in multiple threads.

Since this likely pertains to your last question I had added a comment there: Chip Seq

Answer 1

[Istvan Albert]

Look at the manual here:

https://github.com/usadellab/Trimmomatic

The current trimming steps are:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
LEADING: Cut bases off the start of a read, if below a threshold quality
TRAILING: Cut bases off the end of a read, if below a threshold quality
CROP: Cut the read to a specified length
HEADCROP: Cut the specified number of bases from the start of the read
MINLEN: Drop the read if it is below a specified length
TOPHRED33: Convert quality scores to Phred-33
TOPHRED64: Convert quality scores to Phred-64

it does not look like it offers the option of cutting a specified number of bases from the end

for that purpose you could use other tools like fastp or cutadapt instead