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4 votes
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Nanopore Flongle vs MinION

For us, R10.4.1 Flongle flow cells are running at reduced yield due to lower numbers of working pores (something like 10-20 pores instead of 30-60 pores for R9.4.1 flow cells). This doesn't really ...
gringer's user avatar
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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
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3 votes
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What is Feature Barcoding technology?

"Feature Barcoding" refers to using antibodies linked to specific oligos. The antibodies can then bind to cell surface markers of interest and the oligos they're conjugated with turned into normal ...
Devon Ryan's user avatar
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3 votes

Collapse cell barcodes distribution within 1 Hamming distance

The difficulty with all these things comes with what to do about barcodes that are 1 edit distance away from more than one other barcodes in ways that form complex networks. Cell barcodes are a bit ...
Ian Sudbery's user avatar
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3 votes
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Collapse cell barcodes distribution within 1 Hamming distance

This doesn't use standard unix tools, but rather the API for UMI tools: ...
Devon Ryan's user avatar
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3 votes
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Why are there more barcodes than GEMs in 10X chromium data?

Your initial guess is almost certainly correct. I don't know about the linked read libraries, but in the 10X single cell sequencing protocol, separating real barcodes from noise barcodes is an ...
Ian Sudbery's user avatar
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2 votes
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How to detect mismatch before mapping in RNA-Seq data

At each step in the SLiTing and pooling the barcodes added are not random, but are taken from a predefined list of possible barcodes. When the reads arrive, first you filter by reads that have >1 ...
Ian Sudbery's user avatar
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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
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2 votes
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Why is COI metabarcoding not used for prokaryotes?

The exact answer to your question is bacteria do not have a mitochondrion, therefore cox1 is not a universal gene combining both Archaebacteria and bacteria. In contrast 16S is universal for these two ...
M__'s user avatar
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2 votes

What is the best Query to retrieve DNA from NCBI?

There are two main problems I can see in your approach. First, gene names are not standardized across species and the "same" gene (what that means is a whole different discussion) can have ...
terdon's user avatar
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1 vote
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What is the best Query to retrieve DNA from NCBI?

The search term you need is [gene name] rather than [title]. For example, ...
M__'s user avatar
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1 vote

Find pattern that is present twice and allow <=2 mismatches on each

This isn't perfect but you can build on it to deal with any issues (ie overalpping hits). Also if you need it faster just chunk it and run in parallel threads. I just copy pasted your examples seqs ...
Liam McIntyre's user avatar
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
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1 vote

How to detect mismatch before mapping in RNA-Seq data

It should not be interpreted as "Reads with low quality in more than one base in any of the three 8 nt cell barcodes were also discarded". They only care if the cell barcodes match what are valid cell ...
Devon Ryan's user avatar
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1 vote

What is the --rev_comp_mapping_barcode parameter in the QIIME1 script extract_barcodes.py?

As the help page says: --rev_comp_mapping_barcodes Reverse complement barcode in mapping before lookup (useful if barcodes in mapping file are reverse complements of golay codes) [default: ...
llrs's user avatar
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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
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