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163 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 ...
Cody Gray - on strike's user avatar
32 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 ...
M__'s user avatar
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21 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'...
Zoë Sparks's user avatar
16 votes

What is the difference between samtools, bamtools, picard, sambamba and biobambam?

The obvious answer is that different people wrote them. It's fairly common in bioinformatics for people with a computer science background to get frustrated with existing tools and create their own ...
gringer's user avatar
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16 votes
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Meaning of BWA-MEM MAPQ scores

First of all, if you want to understand mapping quality (mapQ), ignore RNA-seq mappers. They often produce misleading mapQ because mapQ is not important to RNA-seq anyway. Strictly speaking, you have ...
user172818's user avatar
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16 votes
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Better aligner than bowtie2?

Bowtie2 is no longer the fastest aligner. Salmon and Kallisto are much faster, but have been designed to optimise RNASeq mapping. Their speed is gained from avoiding a strict base-to-base alignment, ...
gringer's user avatar
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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".
user6690's user avatar
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15 votes
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Merge hundreds of small BAM files into a single BAM file

samtools merge merged.bam *.bam is efficient enough since the input files are sorted. You can get a bit faster with sambamba and/or biobambam, but they're not ...
Devon Ryan's user avatar
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13 votes
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Obtaining uniquely mapped reads from BWA mem alignment

Update - as of January 2021, samtools can now do filtering based on an expression that includes tag variables. In this case, this expression can be used to exclude any reads that have either an XA or ...
gringer's user avatar
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13 votes
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BLAST(n): No hits found

There are three possible problems that come to mind. Masking Blast will mask low complexity regions by default. Since your sequence is nothing but Gs, it is a safe bet that it is being masked, so no ...
terdon's user avatar
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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.
merv's user avatar
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12 votes

Difference between BWA-backtrack and BWA-MEM

TL;DR: BWA-backtrack is based on backtracking. This approach is appropriate only when the dissimilarity between the reads and the reference is low, or when you want to find all best hits or enumerate ...
Karel Břinda's user avatar
12 votes
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Definition of "seed" in sequence alignment

The seed is the subset of a read used in the first step of an alignment. Many aligners work by a seed-and-extend model, wherein they first find all regions matching the "seed" and then extend the ...
Devon Ryan's user avatar
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11 votes
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Library for computing BWT-based alignments

First, let us remark that there exist several hundred read mappers, most of which have been even published (see, e.g., pages 25-29 of this thesis). Developing a new mapper probably makes sense only as ...
Karel Břinda's user avatar
11 votes
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Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

I'm trying to figure out why. This will be a longer read, Tl;dr at the end: Doing a match There is a good match of Q against ...
voiDnyx's user avatar
  • 401
11 votes
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What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

You are looking for the needle program from the EMBOSS suite. Available in bioconda. http://emboss.sourceforge.net/apps/...
Ian Sudbery's user avatar
  • 3,321
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 ...
Chris_Rands's user avatar
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10 votes
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Counting number of possible alignments between two DNA sequences using python

A closed-form solution is offered in An exact formula for the number of alignments between two DNA sequences by Torres, Cabada, and Nieto: $$f(m,n)=\sum_{k=0}^{min(m,n)}2^{k}\binom{m}{k}\binom{n}{k}$$...
Alex Reynolds's user avatar
10 votes
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How to count the number of mapped read in 100-bp window from a BAM/SAM file

one-liner Here's a gritty one-liner to count the number of reads in a region if you have just one region that you want to investigate. Change the 1 in ...
conchoecia's user avatar
  • 3,181
9 votes
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Aligning many long sequences

Whole genome aliment can be done using Progressive Mauve, LAST or Mummer. For bacteria I used Mauve since it has also very nice visualisation engine. A very new tool is Minimap2, a super fast mapper ...
Kamil S Jaron's user avatar
9 votes

Library for computing BWT-based alignments

BWA-MEM can be used as a library. File bwa/example.c shows the basic functionality for single-end mapping. It should give identical mapping to the bwa-mem command line. Header bwa/bwamem.h contains ...
user172818's user avatar
  • 6,535
9 votes

Difference between BWA-backtrack and BWA-MEM

To quote the Introduction to BWA on sourceforge: BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the ...
Michael Hall's user avatar
9 votes

What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line

Install biopython with conda and use the following script: ...
Devon Ryan's user avatar
  • 19.6k
8 votes

Merge hundreds of small BAM files into a single BAM file

Merging sorted files is a linear operation, so any well-implemented tools that do it will do it with approximately the same efficiency. So samtools merge (use the ...
John Marshall's user avatar
8 votes
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Building STAR Genome Index for nanopore RNA sequencing

The parameter is used to determine how much sequence STAR indexes on each side of a splice junction to improve its alignment accuracy. For very long reads, this may not be ideal. I am not sure if ...
GWW's user avatar
  • 752
8 votes
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Total reads aligning to each reference within a bam file

The quick way to get the number of alignments on each reference is samtools idxstats my_bam.bam Number of reads on each reference is column 3. Although, as has ...
Ian Sudbery's user avatar
  • 3,321
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 ...
Wouter De Coster's user avatar
8 votes

How to get fasta alignment file from SAM/BAM file?

I am not sure what you mean by "fasta alignment file". If you mean a multi-sequence alignment (MSA) in the fasta format, you can't get that because SAM keeps pairwise alignments only and doesn't align ...
user172818's user avatar
  • 6,535
8 votes

Samtools sort: most efficient memory and thread settings for many samples on a cluster

I usually use samtools sort -@4 -m4g. Samtools will be faster with more threads and more RAM, but I feel the gain is not significant. I haven't done a proper ...
user172818's user avatar
  • 6,535
7 votes
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Y Chromosome Aligned Reads in scATAC-seq data from a female-derived cell line?

There are homologous regions between X an Y chromosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region It is therefore normal to have some female-derived reads mapping in Y chromosome. You ...
bli's user avatar
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