Jonathan Moore
  • Member for 3 years, 1 month
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Pipeline to analyse small RNAseq and tRNAs?
1 votes

I have heard that the Small RNA Workbench from UEA can be an easy solution for a full small RNA pipeline. It is java based, has a GUI, and is supposed to be easy to install and run. I am not an ...

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What are the standard ways to visualize protein-protein or gene-gene interactions?
1 votes

Several have mentioned the excellent Cytoscape desktop package for visualising interactions as a graph. If you want to build your own web-based visualisations (rather than using a pre-built website ...

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HVG and variation coefficient
1 votes

There seems to be a dividing line around CoV=0.9. Perhaps this is a good place to start for a cutoff.

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GenomicRanges: get nearest neighbor distances for random genes using a for loop
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1 votes

Is it because rand.gr has not been initialised, so when you ask to set rand.gr[i] it can't because there isn't one yet? If you set i to a value (e.g. 1), and run the lines inside your loop, which of ...

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Method to detect genome doubling
1 votes

The following may work, assuming you have an Illumina genome sequence library with decent coverage, preferably amplification-free: Use kat to produce a kmer spectrum plot of the reads (kmer abundance ...

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Common QC parameters and threshold in human WGS pipeline
0 votes

For your negative controls, you might want to check out QC Fail (https://sequencing.qcfail.com/). There you can see examples of how things look in QC when things have gone wrong, such as loss of ...

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tool to visualize a collection of phylogenetic trees
-1 votes

Dendroscope is worth a look. I would also look into the R phangorn package.

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What do these files / annotations mean?
1 votes

gi looks like a Genbank Identifier. You can search for the 10 digit number following gi| at the Genbank website.

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Is there any way to align ChIP-seq reads to telomeres?
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3 votes

This paper https://www.biorxiv.org/content/10.1101/728519v1.full examines the mapping of some human telomeric sequences, and indicates that there is something like 130kb missing at the telomeres in ...

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Sequencing center returns data in several files
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5 votes

Usually, a single sequencing library is created from each sample. Assuming you are using barcoded indexes to identify multiple samples, the index is attached to each library, and the libraries are ...

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Best way to "fish" long reads that match a query sequence
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3 votes

I have seen the blasr aligner typically used for aligning PacBio reads to a reference. Is there a reason why blasr would not be a good choice? I guess the very short sequence you are trying to align ...

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Find most similar genes to a set of genes of interest in time series RNA-seq data
1 votes

DPGP (McDowell et al, 2018) uses a non-parametric clustering method, so should find clusters without you needing to specify cluster size or number of clusters. It is more or less explicitly designed ...

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Determining the quality of a publicly available genome assembly
1 votes

Carambakaracho's answer is good. A high N50 should usually be a good sign, as well as agreement between the overall genome assembly length and the expected genome size. The number of 'N's in the ...

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Find indels between two short sequences
0 votes

blastn should be able to output this format of alignment result, using the --outfmt 0 option

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Is there a JSON-based genomic feature format?
1 votes

BioJS has capacity to read and write GFF as streams, it might have something of interest such as this: https://github.com/biojs-io/biojs-io-gff

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How does one construct a cladogram of intraspecies relationships?
1 votes

If the accessions have been interbred (conflicting with a tree-like phylogeny), you could try Splitstree, which tries to estimate a tree-like phylogeny with added hybridisation events.

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How to plot character state changes from a presence-absence matrix on to a phylogeny
1 votes

To give some formal words for what you are doing, I would say this sounds like you are trying to reconstruct ancestral states. There has been some work done on this, and a similar algorithm to yours ...

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Appropriate tool or algorithm for sloppy alignment of degenerate bases
1 votes

I believe mafft can align degenerate sequences. From the documentation for version 7 at: https://mafft.cbrc.jp/alignment/software/anysymbol.html Acceptable nucleotide symbols in the default mode: a, ...

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Correlate DEGs from DESeq2, EdgeR and Limma results
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1 votes

I would use the p-value/FDR which each method returns to rank the gene list for that method in order from 'most likely to be DE' to least likely. You would then have three ranked lists of genes - you ...

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How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?
1 votes

Before you proceed, it is usual to do quality control on the .fastq data. The FASTQC program is a good place to start. Once you have checked the quality, trimming is the typical next step to ...

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Hosting IGV web on a server
1 votes

One possibility might be to put the full IGV application on the server, and use the igvR package in R on the server to access the IGV API. You could then use R plotting facilities etc to show your ...

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Find intervals that genes fall within their range
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8 votes

The GenomicRanges package is a great place to start, something like this: library(GenomicRanges) # make a GenomicRanges set corresponding to the genes genes.gr = makeGRangesFromDataFrame(df = genes, ...

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Comparing two genome annotations
1 votes

I would start with metaplots for a visual/exploratory analysis to guide your statistical testing. Cut the genome into short segments e.g. centred on the centre of each nucleosome peak, overlay all ...

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Biological replicates on Chip-seq Transcription factor data
2 votes

You could first look at the degree of correlation between the two replicates - what proportion of peaks are shared between the two, versus peaks found in one sample only? This will give an idea of ...

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Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column
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2 votes

The GenomicRanges package in bioconductor will do this. It lets you do 'set' operations on genomic ranges, such as concatenating them, finding overlaps, etc. Hopefully something in the following ...

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Calculating p-value for introns which are retained (or not) between 2 conditions
0 votes

You might take a look at the MISO algorithm for inspiration, or as a method for calculating confidence intervals of alternatively spliced isoforms: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037023/...

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Loading local FASTA file in igv.js
2 votes

It looks as though the script is looking for a URL (fastaURL) so you could try specifying the file as file://directory/test.fasta By default though, javascript cannot read local files from disk for ...

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Where can I find .cdf files for Affymetrix ChIP-chip data analysis?
1 votes

It looks like it's in GEO here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10187 There is apparently a zipped copy linked at the bottom in the supplementary files. When people upload a ...

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Separation of mixed plasmid DNA sequences post whole-plasmid sequencing
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4 votes

You would expect to have high coverage, given the plasmids are short, so de novo assembly would be likely very easy. Given that each plasmid is present in different multiples, you would expect ...

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How do I perform a pathway related grouping of genes?
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2 votes

The DAVID tool is always interesting, and easy to try: https://david.ncifcrf.gov/gene2gene.jsp You submit a list of genes, it uses several different annotation databases to annotate the gene list, ...

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