removing nextera transposase adapters, cutadapt 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 &lt;any output name&gt; &lt;my input file&gt; 


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 &lt;any output name&gt; &lt;my input file&gt; 


Now, why this is happening? which Nextera transposase sequence is the correct? or am I doing something wrong?
The adapter sequence you have googled is the sequence on the adapter primer. This works when you want to remove primer-dimers.

With transposase adapters or ATAC seq, you have very short fragments and you sequence into the adapter. So what you is sequenced is actually the reverse complement. See below image from trimmomatic manual



So if you look at what worked, and the sequence you googled, they are reverse complement of one another.

You can also see this in the NexteraPE-PE.fa, Trans1 and Trans1_rc @Haci recommended:

more NexteraPE-PE.fa 
&gt;PrefixNX/1
AGATGTGTATAAGAGACAG
&gt;PrefixNX/2
AGATGTGTATAAGAGACAG
&gt;Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
&gt;Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
&gt;Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
&gt;Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC


To answer your question, if most of your fragments are short, and there's not a lot of primer dimers, then yes you are doing the right thing.