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Questions tagged [barcode]

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5 votes
1 answer
75 views

Can index hopping lead to more reads in samples?

We run multiple samples for sequencing on an Illumina NovaSeq machine. After converting the files to fastq format using bcl2fastq, we can see that we have some ...
Assa Yeroslaviz's user avatar
-1 votes
1 answer
99 views

Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads

I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit. I have a question about using Knee Plot for identifying ...
user3377241's user avatar
3 votes
2 answers
78 views

What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
Mirko's user avatar
  • 267
2 votes
1 answer
492 views

Nanopore Flongle vs MinION

How do the Oxford Nanopore Flongle flow cells perform compared to the standard MinION flow cells, when it comes to reliability and error rates? I found this comparison article from last year, from ...
Joel's user avatar
  • 55
3 votes
1 answer
90 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 ...
Joel's user avatar
  • 55
4 votes
1 answer
321 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 ...
nafizh's user avatar
  • 69
1 vote
0 answers
34 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 ...
uvnomad's user avatar
  • 21
1 vote
0 answers
22 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 ...
uvnomad's user avatar
  • 21
1 vote
1 answer
891 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 ...
Trong-Thang Pham's user avatar
4 votes
2 answers
919 views

Collapse cell barcodes distribution within 1 Hamming distance

I have a barcode distribution from single-cell data, e.g: ...
gc5's user avatar
  • 1,813
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 ...
conchoecia's user avatar
  • 3,181
2 votes
3 answers
216 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 ...
gc5's user avatar
  • 1,813
0 votes
1 answer
228 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 ...
user avatar
1 vote
2 answers
157 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 ...
Cyberfox's user avatar
12 votes
4 answers
1k 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 ...
story's user avatar
  • 1,573