I am independently working on data retrieved SRA database, paired-end data as separate inputs. The proceedure I followed is,
- After running FastQC using Galaxy, the majority of the modules have failed.
- I tried Trimmomatic with default settings (Avg quality =20, number of bases to avg across = 4), it resulted in R1 and R2 paired and unpaired (4 total outputs).
- I ran FastQC again, which rendered some changes (per base sequence quality passed) but resulted in other modules (Sequence length distribution and per tile quality scores) getting a warning sign or failing.
My question is,
- Is there specific setting other than default that provides better results? What output should i use from Trimmomatic for fastqc again?