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27 votes
Accepted

How to convert bwa mem output to BAM format without saving SAM file

For directly outputting a sorted bam file you can use the following: bwa mem genome.fa reads.fastq | samtools sort -o output.bam - Optionally using multiple ...
Wouter De Coster's user avatar
12 votes

How to convert bwa mem output to BAM format without saving SAM file

Found the solution. You just need to pipe the output from bwa mem into samtools view like so ...
Michael Hall's user avatar
5 votes
Accepted

Why does BLAST reduce word size for short proteins?

No, the search won't be less reliable. It will only be more sensitive, more capable of finding matches. To understand this, you need to understand how the BLAST algorithm works, what the word size ...
terdon's user avatar
  • 12.9k
5 votes

What is a good multiple alignment of large genome sequences when working with limited hardware?

First of all, do not, I repeat not, use ClustalW. That is horribly out of date and was never very good to begin with1. It was just the first to become common. At least use ClustalΩ. Anyway, while I ...
terdon's user avatar
  • 12.9k
5 votes
Accepted

What is the meaning of "E-value" in the BLAST search?

You can find the definition here: the number of hits one can "expect" to see by chance when searching a database of a particular size. Also read some of the background information given to ...
KingBoomie's user avatar
  • 2,380
4 votes

What is the relationship between a "main" strain genome and its variant genome in archaea?

... I was reading the article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in which they compare the Pyrococcus Furiosus reference ...
acvill's user avatar
  • 8,296
3 votes

What does chrUn mean in the output from a Bowtie run on human sequences?

It is for unassigned sequences. See this reference from the UCSC Genome Browser FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download11
Tara Eicher's user avatar
3 votes

What does chrUn mean in the output from a Bowtie run on human sequences?

I presume chrUn_KI270424v1 refers to a scaffold or sequence that has not yet been assigned to a chromosome. The designation after the Un (unknown or unassigned?) may refer to a particular single ...
David's user avatar
  • 26k
3 votes
Accepted

Confusion about a gene's description

The FAM symbols are defined in the HUGO Gene Nomenclature Committee guidelines. The FAM symbol is an anonymous and temporary identifier that is given to groups of poorly characterised genes which ...
Michael_A's user avatar
  • 1,305
3 votes

What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

They use very different algorithms so they should not have the same E-value. BLAST uses a position-independent substitution matrix (e.g. BLOSUM) while HMMER uses a position-dependent substitution ...
CephBirk's user avatar
  • 233
3 votes

How to compare Smith–Waterman algorithm implementations?

There are only two possibilities for Smith-Waterman alignment with a given cost matrix. It's either right or it's not. Honestly, whatever you're using, it's really really unlikely that a pure Smith-...
Resonating's user avatar
  • 4,058
3 votes

Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I quickly aligned your sequences, and as far as I can tell, the answer is that your "consensus" sequence is a poor match for the 3 other sequences: ...
Maximilian Press's user avatar
2 votes
Accepted

How to interpret Percent identity matrix created by Clustal Omega?

Gene-1 Gene-2 Gene-3 Gene-1 100.00 16.18 20.35 Gene-2 16.18 100.00 29.66 Gene-3 20.35 29.66 100.00 Gene-1 and Gene-1 have ...
WYSIWYG's user avatar
  • 35.6k
2 votes
Accepted

why does the score matrix influence the E value (BLAST)

Perhaps this BLAST tutorial by Steve Altschul will be helpful: The Statistics of Sequence Similarity Scores There is also the BLAST book by Mark Yandell and Ian Korf.
mdperry's user avatar
  • 3,517
2 votes

How to compare Smith–Waterman algorithm implementations?

I imagine that technically your question can only be answered on a computing science Stack Exchange. The pragmatic biology answer is there is no problem. This is such a well established algorithm that ...
David's user avatar
  • 26k
2 votes
Accepted

What factors should I consider when selecting a reference genome for mapping?

There are many reasons! Let's assume you are using the Human reference genome. The latest version is hg38 or GrCh38. This came out roughly three years ago (Dec 2013). Although now these same reasons ...
FoldedChromatin's user avatar
2 votes

How to detect Single Nucleotide Variants (SNVs)?

Your link doesn't link to the paper, and you seem to be ignoring half of what the image is trying to get across. The point is that since tumors are heterogenous, you very well might have only 40% of ...
swbarnes2's user avatar
  • 5,230
2 votes

How to pipe Bwa-mem output without saving SAM file

I never used CIRI2 but I think you can do the same way as I used to pipe with samtools: bwa mem genome.fa reads.fastq | samtools sort -O BAM -o output.bam - So it ...
Thomas Karaouzene's user avatar
2 votes
Accepted

Sequencing inaccurate at the primer site

The very extremities of sequencing reads obtained by most if not all sequencing technologies are usually of lower quality, though more often so in the 5' region. You should disregard this data, or ...
Joe Healey's user avatar
  • 1,301
2 votes

What tool can I use to align multiple protein sequences to one reference sequence?

What you want to perform is commonly called a multiple sequence alignment. As @Wayne_Yux said, the first step is to put all of your protein sequences in a single fasta file. You can then use one of ...
acvill's user avatar
  • 8,296
2 votes
Accepted

What does genetically tractable strain mean?

You've already basically got the idea of "genetically tractable": if we can readily modify an organism's genome using known techniques, then it's genetically tractable. That's a moving ...
jakebeal's user avatar
  • 6,987
2 votes
Accepted

What is the typical arrangement of amplified genes in archaea genome?

You ask "so in the sequence that I linked, should I simply find the sequence of a gene more times if it has been amplified ?" Yes. There are many ways, both natural and artificial, to end up ...
Armand's user avatar
  • 1,721
2 votes

Alignment given two sequence

The poster writes “I need to perform sequence alignment to determine all possible sequence alignments”. It is not clear whether this need is that determined by a course assignment or the poster’s ...
David's user avatar
  • 26k
2 votes

How to calculate the conservation score of specific amino-acids or motifs in a multiple sequence alignment?

Preamble I am not quite sure what the poster is trying to do, in particular the question “is there a way to calculate the score between different disulfide bridges?”. Clearly, if different bridges are ...
David's user avatar
  • 26k
1 vote

Consensus symbols in multiple sequence alignment

The use of these symbols in output of the type shown below is purely presentational, to help you inspect the alignment and identify regions of partial conservation. ...
David's user avatar
  • 26k
1 vote
Accepted

What is the difference between contig- and read-based sequence alignment?

I have never heard the term “contig based alignment”, and your question is the only Google hit of this exact query (apart from a 2012 patent application). That said, and without knowing the exact ...
Konrad Rudolph's user avatar
1 vote

Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?

Most online tools will only help you to design gRNAs for Cas9 because it is the one that is most commonly used. I found an online suite called RGEN tools that also has an option for AsCpf1. However, ...
WYSIWYG's user avatar
  • 35.6k
1 vote

What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?

In your case both answers are equally valid. The scoring matrix, for example DNAFULL (http://rosalind.info/glossary/dnafull/) usually contains various penalties for wrong alignments. Also the ...
Jeppe Nielsen's user avatar
1 vote

Is setting high mismatch and gap penalties sufficient to distinguish perfectly mapping reads?

The preferred way is to map normally and then filter out imperfect matches downstream: ...
user172818's user avatar

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