Hi, I try to trim my sequence with trimmomatic. But I cannot understand why my options are not take account. Indeed input option and output option (check on ouTput files) are not the same. Is there an explanation? Thanks!
Input option:
1Sliding window trimming (SLIDINGWINDOW)
number of bases to average across 6
Average quality required 20
2Cut the specifed number of bases from the start of the read (HEADCROP)
Number of bases to remove from the start of the read 5
3Cut bases off the end of a read, if below a threshold quality (TRAILING)
Minimum quality required to keep a base 20
4Drop reads below a specified lenght (MINLEN)
Minimum lengh of reads to be kept 25
Output option
1Sliding window trimming (SLIDINGWINDOW)
number of bases to average across 6
Average quality required 20
2Drop reads below a specified lenght (MINLEN)
Minimum lengh of reads to be kept 20
3Drop reads below a specified lenght (MINLEN)
Minimum lengh of reads to be kept 20
4Drop reads below a specified lenght (MINLEN)
Minimum lengh of reads to be kept 25