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1500 questions
3
votes
1 answer
Should be RT-qPCR values standardized before PCA analysis?
I come from this question of gene exression analysis: Should PCA be standardized for gene expression?
My experiment is based in 151 x 51 (individuals/samples x genes), in which, patients are subjected to 3 possible groups (~ balanced groups), so we…
Javier Hernando
- 31
- 2
3
votes
2 answers
ERR: error while loading shared libraries: libjulia.so.1: cannot open shared object file [Julia] - Ubuntu 22.04
I'm trying to build a Dockerfile. It has a tool called Atria that utilizes Julia. Since Ubuntu 22.04 does not have Julia package, I had to resort to installing it. The following is the Dockerfile:
FROM ubuntu:22.04
# Install tzdata
RUN apt-get…
pubsurfted
- 333
- 6
3
votes
1 answer
Is there a way I can combine geological data with population genetics data?
So I have ran SAMOVA and made calculations regarding haplotype diversity and nucleotide diversity of several populations. I have also made raster data regarding geographical data like slope, ruggedness etc. Is there a program/package that allows me…
Nickmofoe
- 127
- 4
3
votes
3 answers
What is the correct method of identifying the interacting residues for specific molecular docking?
I'm trying to do a specific molecular docking using Autodock Vina in PyRx. So, one way to do that is to mark all of the interacting residues and make sure the grid box encompasses all of that interacting residues.
So, my protein already has a…
Dembappe
- 61
- 7
3
votes
3 answers
Read Clustal file in Python
This question was also asked on StackOverflow
I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need to import the file and then highlight some…
Denise Lavezzari
- 45
- 4
3
votes
2 answers
DESeq2 for large number of samples takes too much RAM
I am trying to run a very large number of transposase-accessible chromatin (ATAC)-seq samples through DESeq2 to find peaks of differential chromatin accessible across my study genome.
I have about 100 samples, and 1,000,000 "genes" which are really…
Shashank Nagaraja
- 33
- 4
3
votes
1 answer
How to analyse Orthofinder results
I read this paper (Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence). We ran Orthofinder and also created an Upset plot. Unfortunately, I do not…
user3523406
- 165
- 5
3
votes
2 answers
How can I resolve "missing name of population" message in PGDSpider?
I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) Spider, or PGDSpider by Lisher and Excoffier…
Nickmofoe
- 127
- 4
3
votes
1 answer
How to remove double '/' from file path, bash script
I'm using the following script to detect strandedness of my paired end RNA-seq data.
#!/usr/bin/env bash
cd ~/Desktop/fastq
for infile in *_1.fastq
do
base=$(basename ${infile} _1.fastq)
docker run…
pubsurfted
- 333
- 6
3
votes
1 answer
CRISPR genome wide screen analysis using MAGeCK-- Loss of reads/sgRNA using MAGeCK count function?
Sorry if this question seems basic. I am trying to run the MAGeCK pipeline to analyze CRISPR knockout screen data produced by someone in my lab around 5 years ago. I was given the data as bam files and also have the sequencing sample statistics from…
Cassie Bishop
- 31
- 1
3
votes
1 answer
Downloading genes from NCBI in fasta format
I'm pretty new in bioinformatics.
I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download each gene manually from the NCBI database.
The…
Vjon
- 31
- 2
3
votes
1 answer
How to make bar bigger in UpsetR plot
I have tried to use UpsetR to visualize the input file which can be found here.
library("UpSetR")
orthogroups_df<- read.table("orthogroups.GeneCount.tsv", header=T, stringsAsFactors = F)
#All species
selected_species <-…
user3523406
- 165
- 5
3
votes
0 answers
Command line based interaction with the UCSC genome browser, automated data upload and track generation
Is there a way to submit data to ucsc genome browser for result/track display, on the fly, as a local bedgraph file with example contents like below:
browser position chr19:49302001-49304701
browser hide all
browser pack refGene…
Zebra Fish
- 189
- 8
3
votes
1 answer
How to solve Nextflow error: "Trace file already exists"?
When trying to run epi2me-labs/wf-artic, I get the following error:
❯ nextflow run epi2me-labs/wf-artic \
-r v0.3.18 --fastq ~/Downloads/barcode95.fastq.gz \
--scheme_version Midnight-ONT/V3
N E X T F L O W ~ version 22.10.1
Launching…
Cornelius Roemer
- 367
- 1
- 13
3
votes
2 answers
How to extend the x axis in Dimplot Seurat
I have performed a Seurat PCA via Dimplot.
How do I extend the x axis?
As you can see in my figure the double x axes overlap.
cow
- 51
- 3