I am new to the SMART-seq technology, I followed the SMART-Seq® Stranded Kit User Manual by the Takara Bio USA, Inc. After I got my raw data for a sample, I followed the tuxedo pipeline to process the paired end data, FastQC -Cutadapt/Trim Galore - Tophat/HISAT2 - Cufflinks/Stringtie.
For the Cutadapt, I entered my SMART-seq adapters, For each of R1 and R2, I entered my 3' adapter, ATAGAGGC, and 5' adapter GAATTCGT. My quality cutoff is 20, and the minimum length is 20.
Then I got the report:
However, I only got a very small portion of my reads with SMART-seq adapters, read1 with adapters is 6.8%, read2 with adapter is 2.3%. What are the possible problems? Thank you so much.