Community Digest

Top new questions this week:

ggtree:How to keep leading zero ‘0’ in the tiplabel?

I am using ggtree to draw a phylogenetic tree. Some taxa IDs have a 0 at the beginning. However, when I plot the tiplabel the leading zero is automatically dropped. ...

phylogenetics phylogeny ggplot2 ggtree  
asked by YP CHEN Score of 2
answered by M__ Score of 2

How to extract reads that map exclusively to a single site with 1 or zero mismatches from BAM files

I generated BAM files (sorted by coordinates) by aligning human RNA reads against the human reference genome using BWA MEM and ...

rna-seq bam samtools  
asked by plicht Score of 2

Why is the p-value significance threshold for HLA association tests $5*10^{-8}$?

Typically, a p-value of $p<=5*10^{-8}$ is used for genome-wide association testing, as there are roughly $1/p$ independent LD blocks in the human genome, so it correct for multiple testing across ...

statistics gwas p-values hla  
asked by user438383 Score of 1
answered by M__ Score of 1

Running a list of apis via Python's request module

I am running the following Python code with python requests in my Jupiter notebook to get cancer oncology id's from EBI-EMBL. ...

python api python3 jupyter  
asked by Megha Score of 1
answered by M__ Score of 1

Why all values become 1 after dcast?

I am reshaping my dataframe as follows. I want to set the Wavelength column as the column names with the code as follows. ...

r statistics  
asked by YP CHEN Score of 1
answered by Jesse Score of 0

Greatest hits from previous weeks:

changing color key range to specified range in heatmap.2 function

I have a tab separated text file as shown below ...

r bioconductor  
asked by user3138373 Score of 4
answered by Devon Ryan Score of 4

Read length distribution from FASTA file

I have a single ~10GB FASTA file generated from an Oxford Nanopore Technologies' MinION run, with >1M reads of mean length ~8Kb. How can I quickly and efficiently calculate the distribution of read ...

fasta nanopore  
asked by Scott Gigante Score of 27
answered by Sam Nicholls Score of 20

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 Score of 5
answered by Bioathlete Score of 6

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 Score of 6
answered by Kamil S Jaron Score of 13

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...

genome samtools bwa indexing  
asked by annabelperry Score of 1
answered by John Marshall Score of 2

How to show bootstrap values on a phylogenetic tree constructed with RAxML

I apologize for this very basic question. With @Michael G.'s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and ...

phylogenetics phylogeny software-usage  
asked by Leah Score of 1
answered by M__ Score of 1

Uppercase vs lowercase letters in reference genome

I am using a reference genome for mm10 mouse downloaded from NCBI, and would like to understand in greater detail the difference between lowercase and uppercase letters, which make up roughly equal ...

fasta genome  
asked by Scott Gigante Score of 28
answered by rightskewed Score of 26

Can you answer this question?

Is there an R package to calculate global FST, with confidence intervals, for tetraploid populations

I'm interested in estimating global FST among several populations of a tetraploid plant species. I'm looking for an R package that can do this, and can preferably also produce an upper and lower bound ...

asked by steve Score of 1
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