All Questions

1
vote
0answers
18 views

Visualizing Orthologs and Paralogs genes

I ran PorthoMCL but I could not find an explanation about the output format and I would like to visualise the results may be as a circos plot. PorthoMCL contains two output files: Orthologs sample ...
1
vote
1answer
33 views

Why do I have >10,000 cells in the 10X matrix produced by cellranger?

In my scRNA seq experiment, single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3′ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the ...
0
votes
1answer
32 views

Highly variable elements?

Which type of genomic elements in the UCSC browser can be used as an example of the highly labile = highly variable = low conservation regions?
0
votes
0answers
12 views

SCANPY: problem in 3d umap

I would like to project my umap from scanpy in 3d but I have faced the following problem: ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (0,4) and ...
2
votes
0answers
33 views

Protein SCA and DCA

Could you please suggest suitable R packages for statistical coupling and direct coupling analysis of protein sequences? I know there are Python packages for those: SCA and DCA. I was looking for ...
0
votes
0answers
23 views

Is anyone familiar with MathIOmica? [on hold]

Is anyone familiar with MathIOmica and the methodology used by George Mias?
1
vote
0answers
12 views

Possible evaluation or validation of predicted 3D protein structure generated by SCWRL4

I mutated a wild type protein structure using Scwrl4. How can I evaluate or validate the reliability of the predicted structure generated by Scwrl4?
0
votes
2answers
28 views

Proper use of BWA MEM on multiplexed GBS sample

I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads. This yields many individual fastq ...
0
votes
1answer
38 views

Differential expression between two types of cells of specific marker gene expression

I want to define the identity of some cells based on a gene marker (for example the colour yellow< EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the ...
0
votes
1answer
42 views

How to set new identities for new clusters based on a gene expression in Seurat?

I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities. I clustered the cells and then created Violin ...
2
votes
1answer
50 views

Alternative splicing positions on protein

I have mass-spectrometry data (Human cellsanalyzed and annotated by MaxQuant). I want to find which peptides are covering positions of former splice junctions (on the mRNA sequence), based on protein ...
0
votes
0answers
26 views

Queries regarding MetagenomeSeq code

I am trying to understand metagenomeSeq, I will be very much thankful if you could help me to understand this: I do have three treatment condition (T1, T2, and T3) and want to see how these ...
1
vote
1answer
39 views

Tabix queries spanning chromosomes

I can do something like this: $ tabix ${url} ${range} where ${range} spans a region on a single chromosome, e.g., ...
3
votes
3answers
42 views

How can I calculate coverage at single bases using a bam file?

I'm looking for a way to input a vcf or bed file (with specific base positions) and a bam file, and get the coverage at each base position (ie single base bins) using the bam file. I also want the ...
0
votes
1answer
22 views

Where can I find a Data about the average values of gamma-glutamyl transpeptidase in the world? [on hold]

Where can I find a Data about the average values of gamma-glutamyl transpeptidase in the world? I need at least from Muslim countries, european countries and Israel
0
votes
0answers
40 views

RepBase Not available anymore [closed]

kindly choked when i tried to log in into RepBase again and download a Repeat Library but Failed :( the old username was able to login and Download all the required libraries except one, but now when ...
1
vote
2answers
118 views

How to merge .fastq.qz files into a single .fastq.gz with their same id without losing any content in parallel

I have a large number of .fastq.gz files of different lane and reads. I have to merge them each reads group files into single .fastq.gz files. **eg: 1st type NA24694_GCCAAT_L001_R1_001.fastq.gz ...
0
votes
1answer
65 views

What sort of statistic is abbreviated down.rsa and up.rsa? [closed]

I have been asked to analyze an old dataset of cell viability data and was shown a spreadsheet with 7 columns: rep1, rep2, rep1.z, rep2.z, z, down.rsa, up.rsa The replicate counts and z-scores are ...
0
votes
2answers
38 views

Can we use GTEx data as control data for TCGA data?

I am using Recount2 TCGA data and was wondering is it right to use GTEx data as control data for this. I would really appreciate your views on this?
0
votes
1answer
28 views

Which values from Seurat::FetchData function are to be used for correlation analysis between genes?

I want to perform a correlation test between genes in on my single cell RNA seq data set. I perfomed the differential expression analysis using the Seurat version 2 package, after performing stages of ...
0
votes
1answer
26 views

blast command line

I would to use blastx from command line to analize a library produced with RepeatScout in format .fasta to find new transposable elements. I use this command ...
3
votes
0answers
26 views

Determine reference for reference-compressed SRA file

I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the "name not found ...
0
votes
0answers
20 views

galaxy output bam file sorted

I included a new tool in galaxy and I get the following debug msg: ...
0
votes
1answer
34 views

bowtie2 options when mapping stranded single end reads

I'm trying to map RNA-Seq reads generated using the NEB Ultra Directional kit is first strand reversed protocal. I'm using bowtie-2.3.5_1 to align against the mus ...
3
votes
1answer
47 views

Remove variants that do not map to human genome

I received an hg38 VCF file that's had variants imputed with 1000 genomes. I've encountered some issues with the VCF; REF alleles that do not align to a reference genome, ALT alleles that do not ...
1
vote
1answer
47 views

Multi-line efetch digging

I'm using efetch to dig out a middle "envelope" protein within a viral genome specifically within fasta format. The code below works but may not be robust for an entire database. Thus I want to ...
1
vote
1answer
101 views

What do negative dN or dS mean in cal_dn_ds in Biopython?

I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
1
vote
1answer
71 views

How to learn/get started bioinformatics? [closed]

I know this is a broad question and I'm sorry if this is not the right place to post (this is my first post ever), but is there some sort of roadmap for bioinformatics? I'm an undergraduate student ...
1
vote
0answers
42 views

using guppy_basecaller on node with 2 GPUs

I am trying to use the GPU enabled version of the guppy_basecaller on an HPC cluster. I am requesting a node that has 2 GPUs and am requesting 1 of the two GPUs. So, I am trying to set the ...
0
votes
0answers
29 views

Easy filtering seurat metadata based on knn results

Given a Seurat object I'm trying to get the metadata of neighbors cells (knn) to a given cell. I'm trying to create some score for each cell based on its snn neighbors. The score is: ...
2
votes
2answers
44 views

Entrez.efetch returns incomplete genbank records

I am using the biopython Entrez.efetch command to retrieve all features (CDS, mRNA, ...) of some genomes. In this case (NC_014649, Acanthamoeba polyphaga mimivirus), it works as expected: ...
1
vote
1answer
49 views

Align legends to each heatmap in a ComplexHeatmap with 2 heatmaps

I have created a ComplexHeatmap containing 2 Heatmaps, each with their own legend. The legend on the first Heatmap is continuous, whereas that of the second is ...
-2
votes
1answer
69 views

How about BioMoose? [closed]

This is a silly post, but hope it makes a point. We have BioPerl (which never impressed me, in fact there isn't even a BioPerl tag), BioPython (which admittedly is impressive), and even now BioRust. ...
2
votes
0answers
61 views

How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
2
votes
0answers
36 views

find repetitive elements on genome

I'm analyzing mygenome.fa with RepeatScout and RepeatMasker to find transposable elements. I produced a library of Repetitive elements with repeatscout and the I masked TE using Repeatmasker. ...
1
vote
3answers
72 views

Calculate the occurrence of motif in sequences (including overlaps) using Python

I need to calculate the occurrences of a motif (including overlaps) in sequences (motif is passed in the first line of standard input and FASTA sequences in subsequent lines). The sequence name starts ...
1
vote
1answer
48 views

ComBat batch correction: understanding the model

A collaborator of mine is using ComBat for some RNA-seq data. I would like to understand what it's doing, and I have a specific question about the structure of the model. Equation 2.1 of the paper ...
0
votes
2answers
51 views

Reading a txt in R with weird header

I am trying to read a txt file in R but always I am getting ...
3
votes
1answer
20 views

Database for germline copy number variations in cancer

I am interested in looking at germline copy number variations in individuals that are at high risk of developing cancer. Are there any databases where I can look, if a CNV seen in our test case has ...
1
vote
3answers
73 views

Index VCF file for rapid access by rsID?

With tabix one can index a VCF file for rapid variant retrieval based on genomic position. I'm wondering if there are any tools that will index a VCF file to allow rapid retrieval using rsIDs and/or ...
2
votes
2answers
71 views

How is BLAST's nr database created?

Is there a paper or web page describing the procedure for creating the nr database used by NCBI's BLAST implementation? I presume it's some type of clustering, but I'm curious about how exactly ...
2
votes
1answer
51 views

Demographic model for admixed African Americans

I am fairly new to genomics and population genetics. And I am reading this article 'Demographic history and rare allele sharing among human populations': https://www.ncbi.nlm.nih.gov/pmc/articles/...
2
votes
1answer
36 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
1
vote
1answer
30 views

Retrieve ID ligand from PDB file

I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex. Is there a way to do that ...
3
votes
1answer
69 views

Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
-4
votes
1answer
79 views

Finding matched genes for each genomic range

I have called structural variants and now I have ...
1
vote
1answer
59 views

WGCNA error codes in Network Construction & moduel detection

I am using WGCNA and code has worked with no problems with some of my datasets however with most recent attempt when completing gene network & identification of modules. I get following error code....
2
votes
2answers
133 views

Frequency of specific viral sequence in .BAM or .fastq

I was wondering if anyone had any experience 'counting' the frequency of a particular viral sequence in an individual's fastq sequence. So basically, counting the number of occurrences of a particular ...
0
votes
1answer
26 views

Generate table for total number of SV events per sample

I have called and annotated structural variants and I have a table by name of samples and structural events like below ...
1
vote
2answers
67 views

GSEA - Gene Set Enrichment Analysis - in R studio

I have been trying to conduct a classic GSEA using the broad institute software and can not figure out how to compile it in R for the life of me. I am aware that there exists other packages in R that ...

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