All Questions

1
vote
1answer
11 views

What does liability mean in GWAS heritability?

I am reading about GWAS in heritability. They usually say to calculate heritability on a liability scale but after searching for this word "liability", I still don't understand clearly what does ...
0
votes
2answers
26 views

How to convert a gff file to fasta?

I downloaded an annotated genome file in gff format here. I would like to use it for proteomics. Though I need it in fasta format. Is there any tool that converts gff to annotated fasta? I see the ...
1
vote
1answer
24 views

How to quantile normalization on RNA seq counts

I have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it didn't work. I want the result output in matrix ...
1
vote
0answers
11 views

scRNA-seq differential transcript usage

Many of the modern gene-quantification tools (Salmon/Kallisto) output transcript-level (as opposed to gene-level) data. All of the scRNA-seq analysis I have seen just uses the gene-level values. I ...
1
vote
1answer
43 views

data storage requirements for RNA-seq and WGS

Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements?
6
votes
2answers
32 views

How to check if indels in VCF files are left or right aligned?

I download a VCF file from dbSNP, and is curious if the indels in the file are left-aligned for GRCH37 genome. The documentation doesn't say anything. How can we tell if a VCF file has left or right ...
4
votes
1answer
30 views

Albacore basecalling running but outputs 0 reads

I am trying to basecall data produced by the MinION using the SQK-LSK109 kit and FLO-MIN106 flowcell via the command-line. My version of albacore is the latest (v2.3.4). I tried running using the ...
1
vote
0answers
28 views

structural variants: why doesn't AS + AP = SU?

I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples. I have been using SU/AC as one of my filters, looking for variants that ...
0
votes
0answers
11 views

Calculate molecular mass from chemical formula C9H15N4O8P (e.g.) with rdkit?

Can I calculate the molecular mass from a formula like this C9H15N4O8P in rdkit? I think ...
1
vote
0answers
33 views

How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?

How can I prevent a function from sorting my data groups (factors) in alphabetical order without affecting the integrity of the data? I am analysing single cell RNA sequencing data using Seurat 2.3.4. ...
1
vote
1answer
16 views

Parallel in PLINK for linear association for SNP effects

I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used ...
6
votes
2answers
79 views

How do I re-name the headers of my Fasta file?

I appologize for asking this, but I really am really bad with regex... Can someone help me transform the headers of my fasta files from this: ...
4
votes
2answers
51 views

How do you query and explore ENCODE data?

I am looking for a way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an API to ...
0
votes
2answers
116 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
1
vote
1answer
66 views

How to set the position of groups in a Seurat object on a FeatureHeatmap plot

I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on ...
1
vote
0answers
14 views

Circos plot with circlize

This is the post where they made circos using R I'm just following that the part answered by Zuguang Gu, not not sure what I'm doing wrong my file, and the code: ...
4
votes
0answers
26 views

Prediction of prokaryotic origins of replication (ORI)

I want to predict origins of replication (ORI) on hundreds of prokaryotic genomes. The most straight-forward solution would be to use most commonly used tool, Ori-Finder. It uses integrated gene ...
2
votes
0answers
37 views

group samples based on shared mutations in a single multi samples vcf file

I am learning about vcf file formatting and sorry for asking a dumb question. I have a multi-sample (>300) vcf file and I want to group (take) samples with shared mutations. Can someone suggest a ...
1
vote
1answer
78 views

Non-random access on a fastq file

There was a nice question on random access on a fastq file, however I have the opposite problem. I want to programatically access non-random fastq entries quickly (using C++). Say I have several ...
3
votes
1answer
31 views

Sort vcf by contig and position within contig

Due to tabix constraints, I need to sort a vcf so that contigs and then positions within contigs occur in numerical order in the vcf. I don't know if the following will sort positions within contigs, ...
1
vote
1answer
37 views

Calculating Z-score from logCPM values using edgeR

I have the raw counts for RNA-Seq data. I converted counts data to logCPM using edgeR package. Lets say I have a dataframe A with 15000 genes as rows and 100 ...
2
votes
0answers
14 views

What is a sensible forcefield choice for membrane proteins when using PDB2PQR?

I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. There are no lipids in the structure. PDB2PQR has predefined options of amber, charmm, parse, tyl06, ...
0
votes
0answers
13 views

GWAS Retrieve Target Sample from a whole set of samples and PRS in PRSice tool

I am trying to calculate the polygenic risk score (PRS) for the Target Samples in GWAS. I only have the bed/bim/fam file Plink format, after I calculate the SNP effect. Does anyone know how to ...
2
votes
1answer
29 views

How is consensus alignment for OLC assembly usually implemented?

Background In C++ I want to implement a simple class that performs overlap layout consensus assembly but I can not figure out the most logical data structure to use for the consensus alignment step. ...
3
votes
0answers
52 views

Several models identify different which genes are significant

I want to find some good predictors (genes). This is my data, log transformed RNA-seq: ...
2
votes
1answer
39 views

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...
1
vote
1answer
69 views
1
vote
1answer
56 views

Visualising gene expression across cell type and conditions in one plot, in Single Cell Sequencing data

I am new to single cell sequencing data analysis but I have basic programming background in R and python. I want to be able to plot differential expression of two genes, Gene1 and Gene2, across three ...
0
votes
1answer
25 views

log rank p value interpretation from gepia 2

How do i interpret the overall survival when the p value reported is not significant going by the standard convention . Not sure what kind of test it runs while comparing the expression may be one ...
3
votes
1answer
57 views

'Wildcards' object has no attribute 'sample'

I'm using Snakemake and I'm trying to get all my QC reports into multiqc but I get the following error: ...
2
votes
0answers
24 views

How to analyze and visualize CRISPR-CAS9 screening results?

I have a whole-gene CRISPR screening of an assay at different time points. I created a table of the gene number and the count of its reads: ...
1
vote
0answers
17 views

Complexheatmap update issue

After i updated my complexheatmap library i can;t use my old annotation to label sample this is the image how i used to get something like this Code for the below image ...
-2
votes
1answer
76 views

Changing this function to work

I have this matrix of expression data ...
2
votes
0answers
29 views

Ploting FDR along with the pathway as heatmap any simple way

I have this data from one of the cluster which show pathway in context of those genes but when i do a bit of filtering i see plenty of pathways with same or similar FDR which are sort of redundancy i ...
3
votes
1answer
43 views

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
2
votes
1answer
53 views

Drug with as many targets as possible through a system biology graph?

I have 4 pandas data frames containing the following data: affinity_score1: affinity between each couple (Drug-Target) measured using tool1 affinity_score2: affinity between each couple (Drug-Target)...
1
vote
0answers
29 views

amplicon sequencing set up

I have .fastq files from a targeted amplicon sequencing by Illumina MiSeq run. I want to get the target sequences to perform Blast search on them. What is the pipeline to use for processing amplicon ...
4
votes
0answers
12 views

making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)?

Hi I'm a first time user of IADMIX. I tested on one known finnish 1000Genome sample using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is correct. But I'm ...
5
votes
0answers
24 views

Highly heterozygous reads mapping

I have short reads from a highly heterozygous organism (~15% between-haplotype SNP divergence) and I have both reference haplotypes. When mapping the reads separately to each haplotype, I get good ...
-1
votes
1answer
40 views

how to write italic script in Rstudio

I have got the problem on how to write the italic script in RStudio. I used the script in the screenshot and got the error "Error in grobs[[i]]: subscript out of bounds."
2
votes
2answers
95 views

“Sequence Duplication Levels” module still fails after pre-processing Illumina data

I want to ask about why the sequence duplication levels are high after I trimmed by using Trimmomatic? I am using the following Trimmomatic operations: ...
0
votes
0answers
50 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
1
vote
1answer
29 views

Extracting genes differentially expressed by Wilcox test

I have 2 cell types (NOF and CAF) cultures individually and also have been co-cultured with tumour like this picture. https://ibb.co/x8Ty1Wz If this is the log cpm of these 4 samples ...
2
votes
0answers
22 views

convert supplementary reads to primary in sam or bam

I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
-2
votes
2answers
35 views

R package installation in r studio [closed]

I have written a package for my personal use and my other colleagues. I have uploaded the files and source package to different websites. I am able to install the source package in my computer. But my ...
1
vote
2answers
92 views

Genomics Statistics Problem

I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding. I have identified 728 sequences of interest. 597 of these ...
1
vote
2answers
31 views

Using multidimensional scaling to visualize protein sequences by functionality

I have a multiple sequence alignment (MSA) of protein sequences, with which I have performed multidimensional scaling to visualize their clustering. Using R, I used the ...
2
votes
0answers
24 views

Circos plot with mutation data

This was my earlier question but now I would like to see patient sample mutation which i have tried and im getting an output but it looks really dumb So here are my data files and conf file files ...
0
votes
3answers
41 views

How can I install bioconductor-gviz and use it in jupyter notebook?

I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using ...
3
votes
1answer
121 views

Can blat use more than one core/CPU to speed up the alignment?

I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU....

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