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5 views

Gene size and power of detection in sequence divergence analyses

I want to look at violation of the strict molecular clock and compare dn/ds ratio to test differences in evolutionary rates in a set of genes. Some of these genes are really short, is it likely to ...
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0answers
5 views

fgsea returns an empty data frame - How to solve?

I am trying to run fgsea on a vector, v, containing Pearson's correlation. The vector names contain the corresponding gene IDs. When I run the following command, I get back an empty dataframe. ...
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0answers
12 views

protein secondary structure matching/comparison scoring

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: ...
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0answers
12 views

bash loop for strelka2 processing for multiple files from one directory

In the below bash loop for strelka2, 3 bam files are being stored in a variable. The two questions are: Is this proper way to loop through multi bam and wait for ...
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0answers
5 views

Finding simple sequence from reads with significant overlap

I wrote a script to pull out reads from a huge fastq file in an iterative manner, by finding homology to the previous sequence. It seems like it should be relatively easy to overlap them and ...
0
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0answers
7 views

Zuker RNA Folding Traceback Algorithm

I am trying to re-implement Zuker's algorithm for RNA Folding, which considers free energy minimization rather than number of possible pairs in Nussinov's algorithm. I understand how to populate the ...
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0answers
4 views

Recalculating fold change in microarray from a subset of samples

I have some bulk microarray data that I have pulled from online sources which describes the spatial distribution of transcription. The tissue in question has a few different subregions. I am ...
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0answers
5 views

UBCG installation

I wanna install UBCG.JAR in ubuntu 18.04 but I cannot run the java File UBCG.JAR. when I type the code java -jar UBCG.JAR an error message appears. ...
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0answers
8 views

co-expression between LncRNA and mRNA based on P.value and correlation

I have two sets of data, each of which has two treatments with two replications. The first group consisted of 2261 LncRNA (Long non-coding RNA) with FPKM each LncRNA and the second group consisted of ...
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0answers
13 views

How to retrieve dataset names from python statsmodels?

The Python statsmodels library grants access to many R-datasets which can be downloaded e.g. with: ...
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0answers
9 views

How to confirming exon shuffling from genomic sequence, promoter sequence, and mRNA sequence?

I have the genomic sequence, promoter sequence, and mRNA sequence for a novel gene. It is thought that the gene is derived from exon shuffling of multiple genes. How do I characterize each of the 3 ...
2
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1answer
53 views

Bioinformatics flowchart for Materials and Methods

I am going to start work on the Materials and Methods for a paper I contributed to a lot in the bioinformatics processing part. I have seen some papers nowadays tend to first present the processing ...
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0answers
9 views

Search for XL-MS datasets

I am looking for human cross-linking mass spec datasets, where the exact residues that were crosslinked are stated. Any format, say csv, ...
1
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0answers
25 views

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 ...
2
votes
1answer
34 views

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 ...
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0answers
10 views

How can I perform the assumption of the lmfit function from limma package?

I'm doing a DNA methylation analysis using the limma package. The idea is to explore if there is a dose-response between exposure (pm2.5) and methylated CpG sites. Here is my code. I would like to ...
0
votes
1answer
18 views

Clustering information saved in Seurat object

Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to ...
0
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1answer
12 views

Are crystal structure of Ligands used in volunteer computational docking like FightAIDS@home?

In large Volunteer computing for molecular docking projects such as FightAIDS@home, do they use the original crystal structure of ligands in docking or unconfirmed structures of ligand?
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2answers
47 views

Changing the name of elements in a column

I have a very big matrix like ...
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1answer
19 views

Tree cut height for Consensus data input not working

I have tried different combination of tree cut heights but im getting the exprSize as one sample as full the other one as empty . ...
1
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0answers
42 views

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 ...
0
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1answer
30 views

how to interpret of “pvclust” dendrogram and finding height for cutting dendrogram?

I study on RNA-seq expression dataset about one cancer in TCGA. I downloaded FPKM dataset and removed batch effect by ComBat() function. Now, I used pvclust for ...
1
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1answer
21 views

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 ...
1
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1answer
37 views

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 ...
1
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0answers
12 views

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 ...
1
vote
1answer
26 views

Which taxonomy data type to use for abundance graphs and statistical analyses?

At our institution we have had some debate about this topic. So let me give some background: Qiime2 produces a OTU table which shows the number of sequences that matched to a specific OTU. It also ...
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0answers
17 views

How to detail the specific GO terms

How can I get more specific GO terms when using clusterProfiler? I got my Dotplot by: ...
1
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1answer
55 views

move files of a different group to separate directory

EDITED I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For ...
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0answers
14 views

Model matrix design for limma-voom and batch effect correction

I've posted it on Bioconductor but didn't get a response, so I thought maybe I could get some help here (most likely the same audience but I'll try) I have multiple clusters in a 270 leukaemia sample ...
0
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1answer
24 views

Pre-filtering genes for Principal Component Analysis

I have a raw counts data-set of 20,502 genes and 137 samples. I want to find out Principal Components which best explain variation between samples in different stages of tumor. I am new to Machine ...
0
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2answers
33 views

about GO terms's name

Did anyone know whether the GO terms can include more detail information? Like I can get the DotPlot of the GO terms as below: The problem is that some of the genes, in the GO terms, is more about ...
2
votes
0answers
11 views

Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am attempting to write a tool to be used by my lab to automatically generate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
0
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1answer
62 views

Modifying .vcf files

I have 200 .vcf files like this on a Linux system: ...
1
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2answers
23 views

Remove repeated ALT allele from the REF field of a vcf-like file

I have 200 .txt files on a Linux system. In each file, I have the reference allele in the REF column and INDELs in the ...
1
vote
1answer
24 views

Illustrate a 3D visualisation of the three main PCs using plot3d() package in R?

I have a dataset (view/download) here. I need to run PCA on this data set and need to illustrate a 3D visualisation of the three main PCs using plot3d() package. I have looked for more information ...
-1
votes
1answer
21 views

WGCNA module preservation doubt

The WGCNA analysis page48 of that link. In this analysis they are comparing the Preservation of modules between human and chimpanzee brain networks where i see the number of human modules and chimp ...
0
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0answers
36 views

what is the best option for genomic analysis? [closed]

It is best to work with PowerShell, shell script, Pycharm or R for analysis and alignment with Python and R programming language, focusing on genomic analysis, CDS (statistical analysis, database) ...
0
votes
1answer
30 views

Can I use a regular liner regression model when I'm working with DNA methylation data?

I'm new on working with genetics data and I'm just wondering if I can use the lm function when I'm building my models or do I have to use ...
1
vote
1answer
17 views

What software can I use to develop a population haplotype network?

I looking for software to conduct a haplotype network using cytochrome oxidase (CO1) mitochondrial sequence data to study population structure in Anopheles mosquitoes.
4
votes
1answer
54 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
0
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1answer
28 views

Add new tool to galaxy

I am trying to include a new tool to the galaxy main menu, following these instructions. tool_conf.xml doesn't exists only ...
0
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2answers
59 views

how to solve “dim(X) must have a positive length” at running ComBat function in R

I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the ...
2
votes
1answer
39 views

What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?

This question was also asked on Biostars I'm trying to understand what is the best algorithm for GWAS nowadays. I know we have many tools available like Plink and Hail, but currently, what is the ...
0
votes
1answer
19 views

SRA Toolkit and lebanese data

I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218 I installed SRA Toolkit, downloaded the SRR6245218 file and executed this: ...
0
votes
1answer
21 views

How to do the reverse of bcf merge?

How can one do the reverse of bcftools merge? To get one sample back out of the merged one. Without holding reference sites.
1
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0answers
8 views

Can Maven (mass spectrometry software) read mzML files?

I did not find a documentation. Can Maven (mass spectrometry software) read mzML files?
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0answers
44 views

GATK 4.1.4.0 Mutect stats output

I have adapted my pipeline to the new filtering strategies implemented in gatk 4.1.4.0 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number: ...
0
votes
1answer
31 views

How do you map nanopore fast5 files?

Is there a best practices for mapping Oxford Nanopore files to a reference? Is there a tool that can take a tarball of fast5 files and map them directly or do they need to be converted to fastq first?...
2
votes
1answer
38 views

How to quickly and robustly convert between mmCIF and PDB?

There is already a question on PDB/CIF to MMTF, however what is a robust way to programmatically go between PDB and CIF files? For example I can use a python script from this gist that relies on ...
1
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0answers
39 views

TBLASTN error: Too many positional arguments

I was running tblastn using standalone blast2.9.0+ through Ubuntu Linux, to get the alignment result of a list of protein sequences for same species, against its complete genome file. The command I ...

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