Questions tagged [ngs]
use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific tag if applicable (e.g. nanopore, pacbio).
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How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?
In single-cell RNA-seq data we have an inflated number of 0 (or near-zero) counts due to low mRNA capture rate and other inefficiencies.
How can we decide which genes are 0 due to gene dropout (lack ...
2
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1
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Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?
Following this question, I'm confused with the computation of sequence logo
Following data comes from the book "Machine Learning - A Probabilistic Perspective (Figure_1)"
here is the corresponding ...
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Why does the FASTA sequence for coronavirus look like DNA, not RNA?
I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this:
...
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How to simulate NGS reads, controlling sequence coverage?
I have a FASTA file with 100+ sequences like this:
>Sequence1
GTGCCTATTGCTACTAAAA ...
>Sequence2
GCAATGCAAGGAAGTGATGGCGGAAATAGCGTTA
......
I also have a ...
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1
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Which quality score encoding does PacBio use?
Do you know which quality score encoding PacBio uses now? I know some of their file formats have changed in the past year or two, but I haven't found much on their quality score encoding.
The most ...
3
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1
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Metagenomics pipeline recommendations for short-read data
de novo metagenomics on viral NGS data is a hot-topic. On this site alone at least 4 specific algorithms have been used to identify multi-strain/multi-species for a given data set, however these do ...
3
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1
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Is there a publicly available tumor-normal sample?
I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor ...
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Is it possible for coronavirus or SARS to be synthetic?
I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
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How can I call structural variants (SVs) from pair-end short read resequencing data?
I have a reference genome and now I would like to call structural variants from Illumina pair-end whole genome resequencing data (insert size 700bp).
There are many tools for SV calls (I made an ...
15
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1
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Why is bwa-mem the standard algorithm when using bwa?
The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
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What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?
What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.)
For example, I recently received some 10X ...
10
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How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?
How do you generate read-length vs read-quality plot (heat map with histograms in the margin) for long-read sequencing data from the Oxford Nanopore Technologies (ONT) MinION? The MinKNOW software ...
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A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?
Quote:
We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
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How do PCR duplicates arise and why is it important to remove them for NGS analysis?
I am trying to understand PCR duplicates in NGS analyses (actually whole-genome). I searched, and the best answer I found is in this blog.
However I don't understand if I understood how PCR ...
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1
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Extracting sequences from FASTA beginning with common 5' end
I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
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Why are there missing calls in a VCF file from exome sequencing?
My data is a VCF file generated from an exome sequencing variant call pipeline. I'm not very familiar with the sequencing and variant calling process. I noticed that there are some missing genotypes, ...
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How do I validate a single sample ArrayCGH result?
We have arrayCGH (aCGH) results for one sample. There is a 0.5 Mb terminal duplication on chromosome 19 (62995490-63407936, according to NCBI36/hg18). The duplication is rare: a literature review ...
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What is "aligned sequences" and "consensus sequence" in the context of sequence logo? How to compute these?
In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).
so, What is "aligned ...
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Extract reads from bam files by their @RG
How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
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Downloading dataset from SRA (SOLiD Platform)
Trying to download colorspace data from SRA, but getting an error
abi-dump -A SRR1657115.sra
abi-dump.2.9.6 err: item not found while constructing within ...