I know this have been asked in many ways before but I've been struggling a while now so it's time to ask.
I'm trying to use small RNA seq data from: https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-142
These sequences are ~34nt length so they have some kind of adaptor with no doubt.
They use ‘vector strip’ in the EMBOSS package, but I cannot find the suitable vector file.
I've tried with trimmomatic but I still get the same read length
java -jar trimmomatic-0.38.jar SE -phred33 /home/juan/Desktop/juan/bio/mrcv/data/sun/SRR1195024.fastq.gz /home/juan/Desktop/juan/bio/mrcv/data/sun/SRR1195024.trimmed.fastq.gz ILLUMINACLIP:adapters/TruSeq-Small-RNA.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18
I've tried with cutadapt but I still get the same read length
cutadapt -a TGGAATTCTCGGGTGCCAAGG -o SRR1195024.trimmed.fastq.gz SRR1195024.fastq.gz
I've tried with trim galore but I still get the same read length
trim_galore --small_rna SRR1195025.fastq.gz .fastq.gz -o SRR1195025.trimm_gal.fastq.gz
Total reads processed: 14,011,412 Reads with adapters:
8,639,554 (61.7%) Reads written (passing filters): 14,011,412 (100.0%)
Trim galore seems to be doing it's work (61% of sequences with adapter) but then I open fastqc and see that the sequences are not the expected lenght, they're all 34nt.-
I expect to sea a peak in 21 / 24 nt., but it is flat as earth. Any ideas what am I doing wrong?