146 votes
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Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the ...
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46 votes
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Why does the FASTA sequence for coronavirus look like DNA, not RNA?

That is the correct sequence for 2019-nCov. Coronavirus is of course an RNA virus and in fact, to my knowledge, every RNA virus in Genbank is present as cDNA (AGCT, i.e. thydmine) and not RNA (AGCU, i....
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  • 7,284
31 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

This question is quite general, so I'm going to attempt to tie it back to bioinformatics. Background The tree for the current coronavirus is here, showing it is closely related to bat-coronavirus and ...
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30 votes
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Why sequence the human genome at 30x coverage?

The earliest mention of the 30x paradigm I could find is in the original Illumina whole-genome sequencing paper: Bentley, 2008. Specifically, in Figure 5, they show that most SNPs have been found, and ...
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24 votes
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Is it possible for coronavirus or SARS to be synthetic?

The scenarios are impossible and would be laughable if they were not so serious. The evidence is in the phylogenetic trees. Its a bit like a crime scene when the forensics team investigate. We've done ...
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  • 7,284
20 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Some of the other answers here seem quite good; at the same time I think the core answer to the OP's question is maybe a bit hard to tease out of them, so I'd like to try to state it more plainly. It'...
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16 votes
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Why does this human bam file only have one copy of each chromosome?

The maternal and paternal copies of a chromosome are called haplotypes. Many metazoans (animals) are diploid and have maternal and paternal chromosome contribution during sexual reproduction, not just ...
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  • 3,071
16 votes
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What is 'k' in sequencing?

See IUPAC codes: So, as you can see above, K means "Either G or T".
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  • 196
15 votes
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How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?

Actually this is one of the main problems you have when analyzing scRNA-seq data, and there is no established method for dealing with this. Different (dedicated) algorithms deal with it in different ...
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  • 349
13 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Not an expert, but some searching on eukaryotic positive-strand RNA viruses seems to show that polyadenylation is not uncommon. For example, Steil, et al., 2010.
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  • 561
12 votes
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Which quality score encoding does PacBio use?

PacBio does use PHRED 33, but it turns out the question may be irrelevant for the newer PacBio Sequel Sequencer, because it reports all base qualities as PHRED 0 (ASCII ...
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12 votes
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How do PCR duplicates arise and why is it important to remove them for NGS analysis?

In any scenario where depth of coverage is an important factor, PCR duplicates erroneously inflate the coverage and, if not removed, can give the illusion of high confidence when it is not really ...
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11 votes
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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?

UPDATE: The article has now been withdrawn with the following note: This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research ...
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  • 3,462
10 votes
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What is deep sequencing?

I found a post useful for this topic. It explains the difference of coverage and depth. It also has a useful explanation on how to calculate coverage and depth. Here is a copy of what the link says ...
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9 votes

What is deep sequencing?

There are several questions in your post I'll try to answer each one: Is there any way to calculate how deep the sequencing is ? See gringer's answer. TLDR: The depth of the sequencing is how many ...
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  • 4,602
9 votes
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What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

tldr - The I*.fastq.gz file contains the read index sequences. long explanation Illumina uses a program called bcl2fastq to demultiplex sequencing runs. This ...
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  • 3,071
8 votes

What is deep sequencing?

Sequencing depth is typically calculated as the number of total bases sequenced divided by the number of bases in the target genome. An Illumina sequencing run with 2x125 bp reads and 500 million read ...
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8 votes
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Is it possible to perform MinION sequencing offline?

Short answer: yes, but you need to get permission (and modified software) from ONT before doing that. ... but that doesn't tell the whole story. This question has the potential to be very confusing, ...
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8 votes
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Why do I get so many insertions from Minimap2 on my Nanopore WGS?

Insertions and deletions are the dominant error mode of long read sequencing, including nanopore sequencing. What you see is not unexpected. Things may have improved by now if you would download the ...
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8 votes
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Why don't all reads have adaptors?

Things like this might depend on your specific library prep, but in general: sequencing starts at the end of the adapter, not before it. You will only see adapters if you sequence through the entire ...
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7 votes

Why sequence the human genome at 30x coverage?

Solexa Inc. sequenced NA12878 chrX to ~30x in early 2007, which later became part of Bentley (2008). This, I believe, was the first time that 30x showed up. I don't recall they had a particular reason ...
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7 votes

How do PCR duplicates arise and why is it important to remove them for NGS analysis?

PCR polymerases introduce errors. When an error arises in the first few cycles of amplifications, it will appear in a reasonably high fraction of DNA fragments in the library. After sequencing, you ...
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  • 5,735
7 votes

What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing?

There are also third party free and open source basecallers that haven't been developed by Oxford Nanopore. Of particular note is Chiron, which gave the best uncorrected assembly identity among the ...
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7 votes

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?

Normally "inserts" used in the manuscript are "indels" in protein alignments, short for insertions and deletions. What I think has happened is a group investigating indels in HIV env noticed indels ...
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  • 7,284
6 votes
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genes with highest RPKM/FPKM for a human RNA-seq experiment?

As asked as it is, the answer is probably no. Indeed, the highest expressed RPKM/FPKMs will be different from one condition (or tissue) to another one for example. Then, you may also have technical ...
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6 votes

Why sequence the human genome at 30x coverage?

30 times coverage is not unique to this problem, but number 30 has its empirical role in statistics: In statistical analysis, the rule of three states that if a certain event did not occur in a ...
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6 votes
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Can I stop my nanopore sequencing run if there are no more reads being produced?

Yes, you can click "stop acquisition" and your run won't be negatively affected. All of the reads are saved as they are generated. I am not sure how this will impact live basecalling though if that is ...
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  • 3,071
6 votes

Significance and timing of "mux scans"

Yes, your understanding is largely correct. This originates from the situation that for each detector on a nanopore array there are 4 pores. I'll explain mux scans and groups, but this is outdated ...
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6 votes
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Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?

Bits are not frequencies. If a position only contains an A (position 3 for example) then you would need 2 questions (bits) to derive that information without a priori knowledge. Is it a G or C? if no ...
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