We are doing riboseq analysis on some fastq files. We are using Fastp for adapter identification and removal. But, we are facing some problems. fastp is able to remove the adapter sequences only if the adapter seq is given in the command line as an argument. It is not able to detect the adapter and remove it by itself and is giving the output as adapter is not detected. The sra file used, adapter seq and codes are as follows:
SRA file : SRR810103 (fastq size 31.6GB)
adapter seq: TCGTATGCCGTCTTCTGCTTG
./fastp -i ./SRR810103.fastq -a TCGTATGCCGTCTTCTGCTTG -q 33 -w 10 -o./output.fastq ./fastp -i ./SRR810103.fastq -w 10 -o ./output.fastq
Can you please help us?
Eagerly waiting for your help!