How to check for adapters?

Question

[Luna]

I am doing rna-seq analysis of a bacterium and I have done adapter trimming. I have removed the universal adapters , how to find if there are bacterium specific adapters in the reads?

[1769mkc]

run a fastqc on the fastq files, that is the straight forward way

Answer 1

[GenoMax]

how to find if there are bacterium specific adapters in the reads?

There should be no organism specific adapters. Adapters generally come from the kit used to make the libraries.

That said programs like fastp (LINK) and bbmerge.sh from BBMap suite (see --> Identify adapter sequences for trimming from Illumina paired end fastq files ) can help automatically identify adapters, when you don't know the exact library kit used.

[sgupt46]

Is there a way to know if the sequence is a sequencing adapter or UMI?

[GenoMax]

Sequencing adapters would be significantly longer and more common (in terms of numbers) than UMI's.

Answer 2

[Darked89]

You can download UniVec_Core fasta file, then extract primers/adapters (say sequences < 100bp?) and use seqkit locate to search some subset of reads (10-100k) from the intact FASTQ files. This way you may figure out if there are any adapters in your sequences, what these are and the location. At times ppl either on purpose or by mistake do non-obvious things, where read_length > insert_length and you will have a detectable the adapter sequence in large proportion or even all the reads (small RNA i.e.)

[GenoMax]

Original question is about RNAseq analysis of bacterial sample. So I am curious as to how the file you linked (which seems to mostly contain cloning vector and primer sequences) is going to help find adapters (which should be library adapters for purpose of NGS data analysis).

[Darked89]

Well, I have no clue which kit was used to construct the bacterial RNA library, sequence it, possibly with multiplexing. But apart from a ton of obsolete 454/Solid adapters one can check:

 'grep ^>' UniVec_Core | grep Adapt | less