14
votes
Accepted
Fast way to count number of reads and number of bases in a fastq file?
It's difficult to get this to go massively quicker I think - as with this question working with large gzipped FASTQ files is mostly IO-bound. We could instead focus on making sure we are getting the ...
- 861
11
votes
How do I generate a color-coded tanglegram?
I think you can try dendextend, in this manual there is an example of coloring the branches. I don't think it is exactly like your coloring, but with a little tweaking you might get your colorscheme ...
- 3,591
11
votes
Accepted
Tools for simulating Oxford Nanopore reads
Simulators designed specifically for Oxford Nanopore:
NanoSim
NanoSim-H
SiLiCO
ReadSim
DeepSimulator
General long read simulators:
Loresim
Loresim 2
FASTQsim
LongISLND
For an exhaustive list of ...
- 1,939
9
votes
Tools for simulating Oxford Nanopore reads
By chance, just today I've heard of a nanopore read simulator, NanoSim. It is released under a GPL license. I have never used it, though...
- 669
8
votes
How to convert BED to GFF3
To answer the question as asked, for people googling.
For BED6, in python:
...
- 3,341
8
votes
Accepted
How to convert BED to GFF3
Galaxy has API and API-consuming libraries (such as BioBlend) that will allow you to interactively script against it without opening the graphical interface at all.
However you can also take almost ...
- 196
7
votes
Tools for simulating Oxford Nanopore reads
In addition to the already mentioned NanoSim, there is also SiLiCO and ReadSim (although it hasn't been updated in over 2 years, so I am not sure how relevant it is at this point considering how fast ...
- 2,199
7
votes
Fast way to count number of reads and number of bases in a fastq file?
The following is more than twice as fast; however, wc counts newline characters as well. We thus need to subtract the line count from the base count (using Bash):
<...
- 4,895
7
votes
Fast way to count number of reads and number of bases in a fastq file?
pigz | awk | wc is the fastest method
First off for benchmarks with FASTQ it's best to use a specific real-world example with a known answer. I've chosen this file:
ftp://ftp.1000genomes.ebi.ac.uk/...
- 1,069
6
votes
Accepted
tools to reconcile experimental transcripts with reference annotation
I've never tried this myself, so I don't know how easy this is...
One option would be to start with GMAP, which is meant to align whole transcripts against the genome. The really nice thing about ...
- 19.8k
6
votes
Accepted
Visualization tools for 3C/Hi-C long-range interaction data?
I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): HiGlass and JuiceBox.
- 176
6
votes
Accepted
How to convert fastq to fast5
NOTICE:
I have altered my answer slightly from the original as I have turned the original script into a pip installable program (with tests) and have updated the ...
- 713
6
votes
Accepted
How to extract / convert gff3 CDS sequences to multifasta
I like bedtools getfasta. My typical option set is bedtools getfasta -fi <reference> -bed <gff_file> -name -s. Be ...
- 2,584
6
votes
RIP-seq analysis?
You can try doing standard differential expression, but I worry that the between-sample normalization will work poorly. Personally, I would do peak calling instead, followed by diffBind. You have a ...
- 19.8k
6
votes
Accepted
full visualisation of draft genomes alignment
Found a solution, using D-Genies, worked great.
Some examples from their website:
Thanks to @user172818.
- 2,706
6
votes
Is it possible to do this in R?
R supports logistic regression, which would seem to be the most efficient method for tackling this question. Assuming the "Chemo" variable is the type of chemo the code would be something like:
<...
- 161
5
votes
Reordering scaffolds according to a reference without a genetic map
Have you tried Mauve alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds ...
- 965
5
votes
tools to reconcile experimental transcripts with reference annotation
As per my answer to @_julien_roux on twitter:
Trying to find novel transcripts within the context of an existing annotation is much less straightforward. You probably need to do a "genome-guided ...
- 356
5
votes
Fast way to count number of reads and number of bases in a fastq file?
I get fairly quick results with my fastx-length.pl script, with the added bonus of being able to handle multi-line FASTQ files and displaying additional read-length QC statistics:
...
- 14.9k
5
votes
Accepted
5
votes
How to convert BED to GFF3
To convert BAM to GTF, which is the best way to get a file to compare with cuffcompare:
...
- 3,341
5
votes
Accepted
Software recommendation: find DNA sequence distribution over entire transcript
If I understand the question correctly, you'd like to plot the positions of the matches to you motif along with a gene model that shows the positions of introns and exons for the different transcripts....
- 1,816
5
votes
Accepted
problem of "ordering in physical positions" phasing SNPs with Shapeit
The manual suggests that each "chromosome" needs to have its own input file.
You have to split the dataset by chromosomes. ShapeIT can just phase one chromosome at a time. If you are ...
- 2,584
5
votes
How to efficiently compute the exact percentage of non-unique k-mers in a genome for given k?
You can do all of that with khmer. For example, abundance-dist-single.py produces a file with columns: k-mer abundance, ...
- 19.8k
5
votes
Accepted
estimate genome size: kmer-based approach from PacBio reads
I don't think there is a method that would estimate a genome size using raw long reads.
The genome size estimates based on raw reads are done by fitting a model to kmer spectra (for instance ...
- 5,632
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 ...
- 4,254
4
votes
Analysis of differential transcript usage (DTU)
I will take the liberty of giving one possible answers to my own question – but I’m very interested in other answers.
One analysis type that such data enables is the analysis of transcript switches ...
4
votes
How to convert BED to GFF3
Bioconductor makes this so easy. It does the coordinate conversion on import.
...
- 1,603
4
votes
Accepted
Software recommendations - DNA composition
There are more R packages available that calculate GC content, for example Ape's GC.content() function.
For example:
...
- 3,591
4
votes
How to extract / convert gff3 CDS sequences to multifasta
The gffread utility in Cufflinks package might be interesting for you. To generate a multi-fasta file with nucleotide sequences from your GFF file, then you can try:
...
- 2,706
Only top scored, non community-wiki answers of a minimum length are eligible