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8 views

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%...
  • 101
0 votes
0 answers
9 views

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
0 votes
2 answers
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
1 answer
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
0 votes
0 answers
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
1 vote
1 answer
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?
  • 111
2 votes
0 answers
11 views

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 ...
0 votes
1 answer
58 views

convert GT:PL format to GT:GP format

I have a vcf info formatted in GT:PL. ...
2 votes
2 answers
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 <...
  • 21
1 vote
0 answers
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 ...
2 votes
2 answers
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
-3 votes
2 answers
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 ...
2 votes
0 answers
55 views

Adapter trimming

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: ...
2 votes
1 answer
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
0 answers
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, ...
2 votes
1 answer
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 ...
  • 121
3 votes
0 answers
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
0 votes
1 answer
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, ...
4 votes
0 answers
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: ...
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1 vote
1 answer
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: ...
0 votes
1 answer
48 views

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: ...
2 votes
0 answers
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 ...
2 votes
1 answer
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 ...
0 votes
2 answers
58 views

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

I have multiple lists on python: ...
  • 101
2 votes
0 answers
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
2 votes
0 answers
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
0 votes
0 answers
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
1 answer
42 views

How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals

I am trying to split my .bed/.fa file genomic segments into arbitrary smaller overlapping intervals: Consider a typical line/row in my *.bed file as follows: chrom. $\ \ \ \ \ $ start $\ \ \ \ \ \ \ \...
0 votes
1 answer
22 views

Is loss/gain of function reflected in RNA-seq transcript counts?

Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
  • 121
1 vote
1 answer
20 views

Creating multiple phenotype datasets using bootstrap method "Bootstrap-samples-by-column-of-a-data-frame-in-r" for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more ...
1 vote
1 answer
48 views

Where can I download 30x 1000 genomes cram files?

From the preprint published by 1000 genome project (https://www.biorxiv.org/content/10.1101/2021.02.06.430068v1.full) I think the 30x data is for WGS. Can anyone confirm for me if the following file ...
1 vote
0 answers
28 views

I want to map TFBS on to the sequences from dataset containing 8448 (210 base) sequences. its not giving all the hits I need

I want to map TFBS (transcription factor binding sites) on to the sequences from dataset containing 8448 (210 base) sequences, but it is not giving all the hits I need ...
1 vote
0 answers
11 views

Mass spectrometry: How to obtain expression counts for protein

I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent. Each sample corresponds to a folder ...
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2 votes
0 answers
26 views

What data set was used Gene Expression Data of Postmortem Tissues?

I want to run the experiments "Sample Application to Genotype-Tissue Expression (GTEx) Project Gene Expression Data of Postmortem Tissues" mentioned in "Enter the Matrix: Factorization ...
  • 477
1 vote
0 answers
21 views

Naming conventions for kegg nodes with multiple genes

So I'm downloading XML files from Kegg using BioConductor and and I'm running into a problem. If we look at HIF-1 signaling pathway we see the node growth factor (GF) on the left hand side, we can ...
2 votes
1 answer
44 views

What is the best way to process yeast genomes?

I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis. I have a reference genome (S288C) to use for ...
  • 123
2 votes
1 answer
44 views

correlation between imputed genotype and true genotype

There is a graph in the link https://odelaneau.github.io/GLIMPSE/rsquare_eur.html. This graph shows the imputation accuracy of certain MAF bins. Now I understand that $r^2$ is the correlation between ...
2 votes
0 answers
18 views

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
0 votes
1 answer
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
1 answer
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 ...
  • 11
1 vote
1 answer
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: ...
  • 123
1 vote
0 answers
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 ...
3 votes
1 answer
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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3 votes
1 answer
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
0 answers
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/ ...
2 votes
0 answers
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
0 answers
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 ...
  • 11
3 votes
0 answers
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
0 answers
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 ...
2 votes
3 answers
188 views

change/edit FASTA headers

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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