Try running FastQC on you fastq files. It will report if there is adapter sequence (also type of adapter) in your files. Check sample results from FastQC. And then trim your adapters using trimmomatic or cutadapt. Or select the tool according to your data (check Table 1 from this article).

If you know that the sequence was generated using a standard commercial (e.g. Illumina) kit then you could use full set of adapters available in BBMap suite in the resources directory to scan your data.

If that is not the case and if you have paired-end data then you may be able to use bbmerge.sh from BBMap like bbmerge.sh in1=r1.fq in2=r2.fq outa=adapters.fa to identify adapters.

Typically this is difficult to figure out, as not all sequences will have the adaptor, and when it does appear in the sequence it will have different offsets (only the first base, only the first 2 bases, etc). I asked this question a while back and the solution seems to be to give Trim Galore! or similar just a list of all possible adapter sequences, and see what the result looks like afterwards. From this you can probably even figure out what adapter was removed post-hoc. I think there's also something in the BBMap toolkit that can help, but my recollection is that it didn't work on my data for reason (i can't remember, perhaps it only worked when the reads overlapped, or something). But that was some time ago, and BBMap is perhaps one of the most frequently updated suite of tools in bioinformatics right now :)

Really, another question without following up on all previous threads?

• problem with filtering "Sequence unavailable"
• filtering some sequences from txt file in python
• extracting 5'UTR of each gene
• sending big files to other countries
• identifying mutation & copy numbers using sequencing data
• the most frequent isoform of each gene specific to the cell line
• grouping the genes based on the length of coding sequence