Questions tagged [barcode]
The barcode tag has no usage guidance.
11
questions
3
votes
1
answer
51
views
Why is COI metabarcoding not used for prokaryotes?
I'm a beginner in bioinformatics working with environmental metabarcoding, and while reading up on different marker genes, I understand that COI is preferably used for animals thanks to its higher ...
- 33
4
votes
1
answer
309
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 ...
- 69
1
vote
0
answers
31
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 ...
- 21
1
vote
0
answers
21
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 ...
- 21
1
vote
1
answer
737
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
2
answers
770
views
Collapse cell barcodes distribution within 1 Hamming distance
I have a barcode distribution from single-cell data, e.g:
...
- 1,773
2
votes
1
answer
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 ...
- 3,111
2
votes
3
answers
197
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 ...
- 1,773
0
votes
1
answer
212
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 ...
user2197
1
vote
2
answers
154
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 ...
- 13
12
votes
4
answers
901
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 ...
- 1,568