Questions tagged [adapter]

Short nucleotide sequence used by many sequencing methods in order to amplify DNA/RNA fragments, identify DNA/RNA fragments uniquely (Unique Molecular Identifier), anchor DNA/RNA fragments to the flow cell (Illumina). Adapters are useful during the sequencing process and sometimes during data analysis (e. g. indices for demultiplexing, UMIs for removing duplicates) but can be a nuisance and need to be removed prior to downstream analysis, e.g. alignment.

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4 votes
2 answers

relation between Illumina sequencing primer and viral sequences

Dealing whith a problematic sequencing run I found this over-represented sequence: GGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGGCGTCTTCTGCTTG It is clearly relate to the Illumina sequencing primer ...
mox's user avatar
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2 votes
2 answers

Are sequencing reads written differently when inserts and indexes are sequenced seperately?

I was going over different sequencing library protocols and noticed that the adapter sequence can vary between protocols. In some adapter sequences the index sits between the primer binding site and ...
Amos's user avatar
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2 votes
1 answer

Why don't all reads have adaptors?

I got NGS reads back from sequencing platform. I check for adaptors and trimmed them. But I realized only a fraction (eg 30%) have adaptors... why not all of them? Thanks
LauraR's user avatar
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3 votes
3 answers

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 ...
Skepto18's user avatar
5 votes
1 answer

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...
conchoecia's user avatar
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1 vote
2 answers

Why do NEB adapters have non-complementary sequence?

I am making some infographics of different library prep types and noticed something weird about NEB's Ultra II adapters. Molecule 1 is the desired product of the ...
conchoecia's user avatar
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7 votes
1 answer

How to trim adapter sequences from GSE65360 in order to map the reads?

I am trying to map single-cell chromatin accessibility data from doi:10.1038/nature14590, obtained using scATAC-seq, to the reference genome. Example paired-end reads are here. The reads contain ...
firefly's user avatar
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12 votes
4 answers

How can I systematically detect unknown barcode/adapter sequences within a set of samples?

I have often downloaded datasets from the SRA where the authors failed to mention which adapters were trimmed during the processing. Local alignments tend to overcome this obstacle, but it feels a ...
story's user avatar
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