Hi All, I have several smRNAseq data (single end fastq files) and I would like to trim the adapter using trimmomatic, but I am not sure which adapter I have in them. Is there a better way to figure out whether they have NEB-SE, Nextera or TruSeq2 adapter in them?
Here is the command I am using, but I am not sure if that is NEB or Nextera or Truseq.
java -jar trimmomatic-0.36.jar SE -phred33 /media/owner/SeqL008_001.fastq Trimmed_SeqL008_001.fq.gz ILLUMINACLIP:NEB-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18
It looks like there is no adapter(already trimmed) in my sequence below. can someone please confirm? I also want to know if
CATGGC is barcode sequence and if that needs to be trimmed as well?
A<AAFAJF<JJFFJJJFFJJAAFFJFJJJJJFJFJF7J7FF---FFA7FF @K00363:128:HV3CJBBXX:3:1101:2240:1859 1:N:0:CATGGC GGAAGAGCACACGTCTGAACTCCAGTCACCATGGGATCTCGTATGCCGTC + AAFFFJJJJJJJFJJJJJFJJFJJJJJJJJJJJF-J7FFJFJFJJJ-7FJ @K00363:128:HV3CJBBXX:3:1101:2706:1859 1:N:0:CATGGC AAACTTTCAACAACGGATCTCTTGGTTCTGAGATCGGAAGAGCACACGTC + AAFFFJJJJJJJJJJFJJJ-<7-F-FJJFJJJJF<FJJFJJJFFJ-7-AA @K00363:128:HV3CJBBXX:3:1101:2909:1859 1:N:0:CATGGC TCTTGTATTTGGAGAACTCACTCAGATCGGAAGAGCACACGTCTGAACTC + AAFFFJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @K00363:128:HV3CJBBXX:3:1101:2717:1877 1:N:0:CATGGC TGACCTTTCTGTTCCTTTGATAAGATCGGAAGAGCACACGTCTGAACTCC