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8 votes

relation between Illumina sequencing primer and viral sequences

You'll unfortunately find adapter sequences contaminating a lot of entries in Genbank. In short, the sequence is most likely either an unassembled fragment where the input into the assembly step hadn'...
Devon Ryan's user avatar
  • 19.6k
8 votes
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Why don't all reads have adaptors?

Things like this might depend on your specific library prep, but in general: sequencing starts at the end of the adapter, not before it. You will only see adapters if you sequence through the entire ...
Wouter De Coster's user avatar
5 votes
Accepted

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

Question 1: The additional sequences is needed because that is complimentary to the P5 sequence anchored to the flow cell. It is also the site for priming the Index 2 read on a MiSeq. The additional ...
Beth Nelson's user avatar
5 votes

removing nextera transposase adapters, cutadapt

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 ...
StupidWolf's user avatar
  • 1,688
4 votes
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How to trim adapter sequences from GSE65360 in order to map the reads?

First the Nextera adapters and the custom barcode adapters overlap each other ...
Bioathlete's user avatar
  • 2,574
4 votes

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

You mention that FastQC "fails to find the actual adapter sequences" - I guess you mean in the Adapter Sequence Contamination plot. However, the kmer and Sequence Content Plots are often useful even ...
ewels's user avatar
  • 291
3 votes

removing nextera transposase adapters, cutadapt

I cannot quite help(*) on the problem you are having with cutadapt but can point you out to Trimmomatic, for which the ...
haci's user avatar
  • 4,152
2 votes

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

I'm not aware of any existing methods to do this, but here are a couple of ideas about how it might be done: Canu has a method of adapter trimming which involves looking for the absence of overlap ...
gringer's user avatar
  • 14.3k
2 votes

removing nextera transposase adapters, cutadapt

I came across the same problem of Nextera transposase contamination in my shotgun metagenome sequence. I specified the library in trimmomatic and Nextera transposase adapters were successfully removed....
Yike Shen's user avatar
1 vote

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

The order of sequencing in a dual index flow cell is: Read 1 Index 1 (I7) Index 2 (I5) Read 2 Between each step there is a switch of the primer used (Read1-primer -> Index1-primer (I7) -> ...
PPK's user avatar
  • 886
1 vote
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Why do NEB adapters have non-complementary sequence?

Module 3 does not exist during PCR amplification. Here is how NEBNext adaptor and multiplex PCR primers work. During the 1st PCR cycle, only the P7 primers are used to bind and amplify ligated DNA, ...
Pingfang Liu's user avatar
1 vote

Why do NEB adapters have non-complementary sequence?

The original point of the non-complementary sequence is to allow formation of a Y-adapter after USER treatment, since that's what's needed for the Illumina chemistry to work. In reality the bottom ...
Devon Ryan's user avatar
  • 19.6k
1 vote
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How can I systematically detect unknown barcode/adapter sequences within a set of samples?

The minion utility from the kraken/reaper toolkit may be helpful for this: http://wwwdev.ebi.ac.uk/enright-dev/kraken/reaper/src/reaper-latest/doc/minion.html
Nils's user avatar
  • 315
1 vote

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

If you happen to know a sequence that should be highly abundant in the library, you can grep its beginning or end (with pattern match highlighting) and see if the same sequence systematically comes ...
bli's user avatar
  • 3,130

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