Community Digest

Top new questions this week:

Literature mining tools and methods

"As a first step, we sought to systematically establish the complete set of genes implicated in the physiological response to SCI. We conducted a systematic analysis of the SCI literature, reviewing ...

r literature-search  
asked by krushnach Chandra 1 vote

pysam or piping samtools view to a python script

Is it faster to use the PySam package to run a python script on a bam for read in samfile.fetch('chr1', 100, 120): print read compared to using a pipe and reading line by line from stdin in a ...

samtools pysam  
asked by Stav Grossfeld 1 vote
answered by Devon Ryan 2 votes

Interpreting quantitive outputs from maximum likelihood phylogenetic trees

I ran a calculation in RAxML to determine the majority consensus phylogeny of a maximum likelihood bootstrap (How to show bootstrap values on a phylogenetic tree constructed with RAxML), and I got ...

phylogenetics software-usage  
asked by Leah 1 vote
answered by Michael G. 1 vote

Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...

statistics single-cell modelling linear-regression multi-omics  
asked by tebiwankenebi 1 vote

Which of these enzymes is a better target for virtual screening?

I am a MSc student in Applied Biochemistry. For my Masters Thesis, I will be doing some research about finding new potent inhibitors for a specific enzyme of my choice using molecular docking (virtual ...

docking molecular-genetics  
asked by Linda 1 vote
answered by Matteo Ferla 0 votes

How can I get the estimate of lmFit function form limma package

This is the first time that I used lmfit function from the limma package and I'm a little bit confused on how to interpret the result. Also, is there a way to get the estimate or the beta from lmfit

dna limma methylation  
asked by Mr.M 1 vote

Greatest hits from previous weeks:

How to extract fasta from a blastdb

How to extract the sequence used to create a blast database. This is useful when you download a blastdb from somewhere else e.g. one of the databases provided by NCBI including the 16SMicrobial ...

fasta blast  
asked by amblina 4 votes
answered by amblina 3 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a ...

python dna benchmarking  
asked by conchoecia 13 votes
answered by Devon Ryan 16 votes

Formula for k-mer coverage

Let $C$ be base coverage, $R$ is the length of reads and $K$ is the length of $k$-mer. Then $k$-mer coverage $C_k$ can be computed as $C_k = C\cdot(R - K + 1)/R$. Could someone please explain why is ...

asked by user44697 8 votes
answered by Devon Ryan 3 votes

Seurat with normalized count matrix?

I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix according to the documentation. I have only the already normalized count ...

r seurat  
asked by Nikita Vlasenko 2 votes
answered by burger 4 votes

How to extract / convert gff3 CDS sequences to multifasta

I would like to extract all the CDS from a batch of genomes. I have found a perl script from BioStars but this does not seem to work for me. I would preferably like to have a script/ method which will ...

fasta software-recommendation format-conversion gff3  
asked by AudileF 5 votes
answered by Bioathlete 4 votes

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart. I tried to get a kind of conversion table for all human genes. ...

gene public-databases biomart conversion  
asked by floatingpurr 4 votes
answered by Ian Sudbery 4 votes

Volcano plot in R

This question has also been asked on biostars How can I reproduce this volcano plot? I'm only able to do the traditional one, I'm kind knew too these field.

rna-seq r visualization  
asked by Sofia 6 votes
answered by Kamil S Jaron 11 votes
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