14 votes
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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 ...
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  • 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 ...
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  • 3,551
11 votes
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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 ...
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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...
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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 ...
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  • 2,099
7 votes
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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 ...
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  • 186
6 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): <...
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6 votes
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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 ...
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  • 19.2k
6 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/...
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  • 1,029
6 votes
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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.
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  • 176
6 votes

How to convert BED to GFF3

To answer the question as asked, for people googling. For BED6, in python: ...
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  • 3,221
6 votes
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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 ...
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6 votes
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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 ...
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  • 2,566
6 votes
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full visualisation of draft genomes alignment

Found a solution, using D-Genies, worked great. Some examples from their website: Thanks to @user172818.
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  • 2,646
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 ...
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  • 925
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 ...
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  • 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: ...
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  • 11.8k
5 votes
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How to convert GFF3 to GTF2

The following bit of python code should work: ...
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  • 19.2k
5 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 ...
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5 votes
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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....
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  • 1,806
5 votes
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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 ...
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  • 2,566
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, ...
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5 votes
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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 ...
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  • 5,327
5 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: <...
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  • 151
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 ...
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  • 3,719
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 ...
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4 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: ...
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  • 3,221
4 votes
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Software recommendations - DNA composition

There are more R packages available that calculate GC content, for example Ape's GC.content() function. For example: ...
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  • 3,551
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: ...
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  • 2,646
4 votes
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RIP-seq analysis?

You need to be careful of terminology. To me, a RIP-seq experiment involves a pull down, followed by a RNAseq library prep. Thus, the whole transcript is captured, not just the binding site of the ...
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