162
votes
Accepted
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 ...
- 1,486
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__♦
- 10.2k
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'...
- 319
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 ...
- 13k
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 ...
- 6,295
16
votes
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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 ...
- 19.5k
15
votes
Accepted
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, ...
- 13k
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 ...
- 13k
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 ...
- 9,352
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.
- 621
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 ...
- 1,899
12
votes
Accepted
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 ...
- 19.5k
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 ...
- 1,899
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 ...
- 401
11
votes
Accepted
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/...
- 3,271
11
votes
Accepted
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 ...
- 3,858
10
votes
Accepted
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:
$$f(m,n)=\sum_{k=0}^{min(m,n)}2^{k}\binom{m}{k}\binom{n}{k}$$...
- 3,105
10
votes
Accepted
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 ...
- 3,111
9
votes
Accepted
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 ...
- 5,467
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 ...
- 6,295
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 ...
- 643
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:
...
- 19.5k
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 ...
- 946
8
votes
Accepted
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 ...
- 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 ...
- 3,271
8
votes
Accepted
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 ...
- 1,304
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 ...
- 6,295
7
votes
Accepted
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 ...
- 3,070
7
votes
The effects of incomplete bisulfite conversion upon mapping efficiency
Bisulfite conversion efficiency has no effect on the mapping rate in bismark and similar tools. The reason is that the reads are fully bisulfite converted in silico before alignment to minimize ...
- 19.5k
Only top scored, non community-wiki answers of a minimum length are eligible