27
votes
Accepted
What is a quick way to find the reverse complement in bash
Thanks to Manu Tamminen for this solution:
echo ACCTTGAAA | tr ACGTacgt TGCAtgca | rev
- 2,166
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
12
votes
Accepted
Least present k-mers in the human genome
You can use the Jellyfish software to calculate the k-mer profiles up to length 31.
From the instructions in the user guide:
The basic command to count all k-mers is as follows:
...
- 2,574
10
votes
Least present k-mers in the human genome
You can also use R. I give you an example of only chr1 and only kmer=4.
...
- 3,561
8
votes
Accepted
Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?
using a http request.
if there is a DAS server, you can always use this protocol to download the xml -> fasta. see https://www.biostars.org/p/56/
...
- 1,481
8
votes
Accepted
Calculating average coverage for .bam files (sequence data)
For a quick estimate you’re making it more complicated than necessary.
The theoretical average coverage is $\frac{n \cdot \hat l}{N}$ where $n$ is the number of reads, $\hat l$ is the average read ...
- 4,815
7
votes
Accepted
Generic HMM solvers in bioinformatics?
I would also recommend to take a look at pomegranate, a nice Python package for probabilistic graphical models. It includes solvers for HMMs and much more. Under the hood it uses Cythonised code, so ...
- 171
7
votes
What is a quick way to find the reverse complement in bash
Reverse complement FASTA/Q:
seqtk seq -r in.fa > out.fa
https://github.com/lh3/seqtk
- 79
6
votes
Python API for working with ENSEMBL genomes
Now there's another option, the ensembl_rest module, a thin wrapper around the Ensembl REST API to simplify its usage and make it more pythonic. You can find the ...
- 61
6
votes
Accepted
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 ...
- 574
6
votes
Accepted
How to understand methylation level?
You are right that a single molecule in a single position is either methylated or not methylated. However:
First, assuming your organism of interest is diploid (or of higher ploidy) one of the ...
- 1,304
6
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 ...
- 6,295
5
votes
Identifying relevant SNPs from a list
What you are looking for is SNP annotation. If you have the chromosome:position reference and alternate alleles for your SNPs of interest, it can be as simple as uploading them to the variant effect ...
- 393
5
votes
5
votes
Generic HMM solvers in bioinformatics?
There are certainly software libraries for working with HMMs. For a general-purpose implementation in C++, take a look at the SeqAn HMM algorithms.
For your purposes, i.e. “computing … the most ...
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5
votes
Accepted
What is "aligned sequences" and "consensus sequence" in the context of sequence logo? How to compute these?
Panel (a) shows a sequence gap-free alignment. Each row corresponds to a contiguous 15 base pair sequence of DNA (e.g. row 1 could be a human sequence, row 2 could be the equivalent mouse sequence etc....
- 3,858
5
votes
Accepted
How to compute the Shannon entropy for a strand of DNA?
Why do you think the entropy of 0 is incorrect? It intuitively makes sense, as there is no uncertainty about the base at position 3, and thus there is no entropy.
However, what is plotted in a ...
- 360
5
votes
Understanding some of the computational bottlenecks of Covid-19 research
I can only speak of drug design (and even then I am terrible at turning down the jargon).
In the case of drug design, this is pretty much plan C. Namely, none of compounds that entered clinical trial ...
- 4,124
5
votes
How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
I would just blast it. When blasting locally, you need to first make a database from your genome, so assuming you got the command-line version of blast installed you can do something like
...
- 5,467
4
votes
Generic HMM solvers in bioinformatics?
If I remember correctly Ewan Birney's Dynamite (a compiler-compiler) as presented at ISMB 1997 had this functionality, there is also some code here on GitHub https://github.com/birney/wise3 which at ...
- 1,049
4
votes
Accepted
Is it wise to use RepeatMasker on prokaryotes?
If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools.
...
- 957
4
votes
calculating nucleotide frequency per column
Here is one example of how to do this with a bit of python. Alternatively one could create strings of each column and using letterFrequency() from the ...
- 19.5k
4
votes
4
votes
Combine Fastq by writeFastq is not working properly
You can drastically simplify your effort because FASTQ files are simple text files; therefore, standard UNIX test file tools work:
...
- 4,815
4
votes
Books on bioinformatics algorithms
Here are a couple books I'd recommend:
Dan Gusfield's Algorithms on Strings, Trees, and Sequences is a deep and wide treatment of aligning, searching, and processing strings, trees, and sequences.
...
- 3,105
4
votes
Accepted
What is cellranger doing in comparison to other methods?
cellranger mkfastq is not necessary anymore. It used to be that the cellranger software wanted the reads to be interleaved, and you could use cellranger to do that for you if you couldn't do it ...
- 1,812
4
votes
Accepted
Python API for working with ENSEMBL genomes
The correct API for Ensembl is the Ensembl REST API which is updated and maintained by Ensembl, and language agnostic.
- 1,739
4
votes
Hardware Requirements (specs) for Bioinformatics-dedicated desktop
The RAM requirements for some bioinformatics analyses like assembly can be quite high (in the hundreds of Gigabytes). My recommendation is to get a fast laptop. Something with an i7 quad-core ...
- 2,166
4
votes
Accepted
CDS length for each human gene
While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for ...
- 9,352
4
votes
Accepted
Generating DNA sequences with constraints
You can use a $l$-order Markov chain. Here is the procedure:
Count $l$-mers in your genome. For small genomes, you can do that in Python. For large genomes, you may need jellyfish or KMC3.
Draw a $l$-...
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