I am learning about NGS analysis and im currently learning about QCing and removing adaptors.
I am working on SRR1972920_1.fastq file.
When running fastqc tool on that file, adapter contamination is present in the form of Nextera Transposase adapters.
Searching for that adapter sequence via google the sequence for at the 3' end to be removed is TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG (obtained via illumina adapter sequence-Nature).
Running a very basic cutadapt command line to remove the adapter
cutadapt -a TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -o <any output name> <my input file>
After running the fastqc tool again on the new output file from cutadapt, it seems nothing changed and the contamination still present.
However, when running the same command above but changing the sequence to CTGTCTCTTATA, which is the sequence of transposase adaptors according to fastqc tool adapters_list.txt file all is good after running fastqc tool on the file
cutadapt -a CTGTCTCTTATA -o <any output name> <my input file>
Now, why this is happening? which Nextera transposase sequence is the correct? or am I doing something wrong?