Questions tagged [barcode]

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4
votes
1answer
54 views

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

I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...
0
votes
0answers
21 views

Generating taxonomic hierarchy by species/genus name

I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
1
vote
0answers
18 views

mining DNA barcodes from Genebank/BOLD per location

Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
1
vote
1answer
365 views

What is Feature Barcoding technology?

I heard the term Feature Barcoding a lot so I find resources to understand it. I have read docs of 10xgenomics and I see that ...
4
votes
2answers
507 views

Collapse cell barcodes distribution within 1 Hamming distance

I have a barcode distribution from single-cell data, e.g: ...
2
votes
1answer
1k views

Why are there more barcodes than GEMs in 10X chromium data?

Question: Why are there more barcodes than GEMs in 10X chromium data? Introduction I have several 10X genomics chromium libraries made with the de novo assembly/genome protocol. The 10X chromium ...
2
votes
3answers
159 views

How to detect mismatch before mapping in RNA-Seq data

In the methods of this paper, the authors say: Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
0
votes
1answer
170 views

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

I'm using the QIIME1 scripts extract_barcodes.py to extract barcodes from a dual-indexed MiSeq library, and then demultiplex my reads using split_libraries_fastq.py. I have been having trouble ...
1
vote
2answers
132 views

Workflow of metabarcoding analysis

For a diet analysis of an insect-eating animal, all species in a sample shall be identified. For this a sequencing of the metagenomic sample was done, where the COI/COX region was used as a barcode ...
11
votes
4answers
632 views

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 ...