# All Questions

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### Searching for HLA-B in DNA results

I'm trying to find the HLA-B*15:01 variant in my DNA results, prompted from this research paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8142661/#:~:text=HLA%2DB*15%3A01%20is%20strongly%...
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### Looking through subdirectories biopython and compare to another file

I want to compare a text file to records in different subdirectories. How to get absolute path and compare them? python
25 views

### How can I assemble my genome from raw files?

I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF). How can I assemble it? And does assembly provide any further ...
1 vote
15 views

### KEGG retrieve hierarchy for organism in biopython

I want to obtain a direct graph from KEGG as well as the genes present in a single term. While it is pretty easy to get list of genes/compounds that are part of a specific category, I am kinda stucked ...
• 21
10 views

### Cannot run loadData() after saving RDS file and reading RDS file using saveRDS & readRDS in Seurat

I want to load multiple sample data(pbmc16 and pbmc45), and integrate by following the tutorial below Performing integration on datasets normalized with SCTransform https://satijalab.org/seurat/...
1 vote
32 views

### Visualize RNA co-folded secondary structure with Python

I would like to visualize the secondary structure of co-folded RNA strands in Python, preferably in a Jupyter notebook. What are the recommended tools? Can anyone provide an example?
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### I am trying to use slingshot for pseudotime analysis. I am getting error while saving an object as dataframe

When I run following code, I get error at - slingshot_df <- data.frame(colData(sce)) the error is : Error in as.vector(x) : no method for coercing this S4 ...
58 views

### convert GT:PL format to GT:GP format

I have a vcf info formatted in GT:PL. ...
50 views

### Parsing a genbank file and outputting specific feature information to a csv using BioPython

So I am trying to parse through a genbank file, extract particular feature information and output that information to a csv file. The example genbank file looks like this: SBxxxxxx.LargeContigs.gbk <...
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1 vote
10 views

### Recode bgen files against reference genome

I have a set of .bgen files split by chromosomes, including both SNPs and INDELS (named with both rsids and chr_pos_a1_a2). I know a large portion of them are encoded on the wrong strand, and I want ...
42 views

### WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low

I'm doing a WCGNA analysis (signed network) on microbiome 16S data. I have transformed counts to centeres log-ratio transformed data (CLR) to address the compositional characteristics of the data and ...
• 21
62 views

### Finding virulent strains of viruses by alignment using databases [closed]

Kindly help me how to find a virulent strain of a virus by aligning the sequences in the databases. I am looking for a virulent strain of a virus by aligning the sequences in the databases and ...
55 views

I am trying to do adapter trimming, alignment and sorting for a range of large scale paired end fastq files. The code I am using is given below: ...
19 views

### need bam file for pilon

I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file. How do I make a BAM file of the resulting assembled.fasta?
• 123
1 vote
14 views

### Comparing common genes and transcripts between Gencode and Refseq

This is a very naive question - I am trying to compare and get the common lncRNA genes and transcripts between Gencode and Refseq from their gff files. Since their gene_id, gene_names are different, ...
22 views

### Coordinate numbering between forward (+) and reverse (-) strand in Tombo

My question is related to the output of Tombo re-squiggling algorithm on nanopore data. Given the position/coordinate on one strand (+ or -), I want to find the coordinate of its exact location on the ...
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36 views

### Aligning PacBio HiFi reads to reference genome using pbmm2

I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
• 123
25 views

### Building a group representation of genes' ontologies

I have a list of genes (about 2000) from lines of drosophila subobscura, in the following format: LOC117900589 LOC11788959 LOC11790331 I'm trying to represent this set of genes in a useful way. So, ...
• 169
73 views

### Write a bash script to run gatk, fix errors with input, and rerun until completion

I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating: ...
• 41
1 vote
46 views

### Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF

I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this: ...
• 281
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### Merge/Join one data frame (X) to multiple data frames separately

Let us say that we have some data frames named S1,S2,S3... that I want to join independently by column names to dataframe X. This is how they look like: ...
18 views

### Avoiding false anticorrelations between individual genes per cell in single-cell RNAseq

When analysing a single-cell RNAseq dataset, one question I like to ask is: At a single-cell level, are these two genes correlated (expressed together) or anticorrelated (only one or the other is ...
• 121
56 views

### How to calculate average BLOSUM62 scores?

I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids. However how would you calculate the average ...
58 views

### How to merge multiple list into a single dataframe replacing common values with 1 -python

I have multiple lists on python: ...
• 101
37 views

### What codes represent what genes?

I want to run experiments on the data used in PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF link So far, the paper has reduced the dimension to ammon's ...
• 477
18 views

### MAGs transcriptomics pipeline question

I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
• 53
19 views

### Relationship between molecular weight and linear peptide

Sorry for this very beginner homework question: Which of the following linear peptides is consistent with Spectrum = {0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332 333}? (Select ...
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1 vote
42 views

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### snRNA-seq Demultiplexing before or after QC

I'm currently analyzing snRNA-seq data and have to demultiplex them using HTODemux in Seurat. The question is : should I do my QC filters on my droplets before or after the demultiplexing ? From what ...
• 21
57 views

### Single or partitioned model for supermatrix tree inference?

I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
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1 vote
39 views

### Advise on building an effect ML model for predicting important proteins for drug response

I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
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1 vote
46 views

### Fixing FASTA file for Local BLAST Database

I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format. Each individual FASTA file looks something like this: ...
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1 vote
30 views

### Cancer: computing the proliferation of DNA mutations in cancer cells [migrated]

I have a question about cancer. How is it, that in a cancerogenous cell, once a specific gene changes, subsequent DNAs in cells end up exponentially acquiring more and more mutations? Can, these ...
54 views

### Is there an alternative to bulked segregant analysis for insects?

This strategy seems to be most commonly used for plants. When crossing animals isn't possible, how can I do a similar study to identify a particular locus responsible for a polymorphic trait (...
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38 views

### How does one distinguish nuclear DNA from mitochondrial DNA when doing WGS?

I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene ...
• 247
1 vote
12 views

### Do proper .fcs flow-cytometry files specify the gating hierarchy, so one may calculate cell-counts without specifying it themselves?

Do proper .fcs flow-cytometry files already have the gating hierarchy, so one may calculate cell-counts without extra work? https://github.com/whitews/FlowKit/ ...
21 views

### How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?

How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files? The way flow-jo exports is in wide rather than ...
1 vote
11 views

### Can we use different cell filter in different single cell R package (monocle and Seurat)

I was confused about whether we can use different subset parameters in data preparation. In Seurat used ...
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27 views

### How to select the best ligands in a virtual screening matrix

I have the results of a virtual screening experiment using docking simulations with Autodock Vina. The result is a matrix of 7 (proteins) by 28000 (ligands) with the calculated binding energies for ...
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1 vote
30 views

### How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
188 views

I have a FASTA file with 97,000 entires arranged like this : >tr|A0A075B6G3|A0A075B6G3_HUMAN Dystrophin OS=Homo sapiens OX=9606 GN=DMD PE=1 SV=1 I want to have ...
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