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26 views

Nanopore variant calling

So far I haven't done any variant calling as such. Nanopore I have used for 16s microbiome data. Now My question/doubt so how do I proceed for nano-pore virus sequencing data Steps: I get fast5 files ...
1
vote
0answers
11 views

How to chose values for QC for a GWAS?

I am running a GWAS on a large dataset. I am using the H3aBioNet QC workflow (https://github.com/h3abionet/h3agwas/blob/master/qc/README.md). I have run the QC on initial parameters: MAF < 0.01 ...
0
votes
0answers
7 views

Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus

This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this step that keeps stumping me. I'm ...
0
votes
0answers
12 views

Why use shuffled input-sequences as background of MOTIF discovery? (from CLIP-seq data using MEME-suite)

By default, STREME (MEME-suite) uses second-order shuffles of the input sequences as background. STREME highlights its usefulness for CLIP-data, which would be my origin of sequence-inputs. In this ...
1
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2answers
47 views

Reading in external single cell data

I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix. counts found here: https://www.ncbi....
0
votes
2answers
21 views

What are some ways to check metagenomic bin quality?

I am new to metagenomic binning. I've used CheckM in order to estimate completeness and contamination values, and most of my bins of interest appear to have good values. My workflow was pretty ...
1
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2answers
25 views

Offline Interactive Genome Map

I use the CGView Server for constructing circular genome maps. It is really a convenient tool for me to explore circular genome maps because it's interactive. I can search a certain region and it can ...
0
votes
0answers
15 views

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these? For the moment I ...
1
vote
0answers
11 views

maxEE parameter from DADA2 package in R

I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails. I have surfed many forums, as well as the details given by ...
0
votes
0answers
24 views

Extracting Sequence Unique to a Certain Genome

I have two genomes with high similarity. But I found out that one genome has a longer sequence of about 200 kbp. I try to align the sequence with Mauve. How can I extract this unique 200 kbp?
0
votes
1answer
28 views

Calculating dn/ds ratio between two model organisms

I am trying to calculate the dn/ds ratio between the human genes and c.elegans. However, I am getting NA values in the output file I used the following script ...
0
votes
0answers
22 views

Error generating count data using featurecounts in R

I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
0
votes
3answers
32 views

Polishing PacBio or ONT with Illumina

Which tool would be good to polish PacBio or ONT with Illumina? Thank you in advance
1
vote
0answers
18 views

Definition of Copy Number Abundance

Reading from this paper: The remaining 9 new copy-number alterations showed altered coverage patterns on whole-genome sequencing but could not be confirmed by orthogonal methods because of their ...
0
votes
0answers
26 views

Phasing genotyped data using shapeit: ERROR: Wrong ordering in physical positions

I am to phase my genotyped data with Shapeit (from ped or bed files) and I keep on getting this error message: ERROR: Wrong ordering in physical positions curr_pos=13915 prev=157299737 Any idea on ...
1
vote
1answer
33 views

bowtie No alignments

This question was also asked on Biostars hi all, I am working on miRNA alignment using bowtie. But it seems to fail to map. Here are the commands: ...
3
votes
1answer
42 views

Updating the GFF3 + Fasta to GeneBank code

I'm trying to convert gff3 and fasta into a gbk file for usage in Mauve. I've found a solution but the code is outdated: ...
0
votes
0answers
17 views

How to identify in a RNA seq data in which sample is in which cell using R using qusage

I am using RNA seq data and have been using QuSage in R in hopes to try to identify different samples and figure out which cell it belongs to. I am trying to visualize and utilize the results but I am ...
1
vote
1answer
40 views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
0
votes
1answer
14 views

Publicly available genotype / phenotype dataset?

I'm looking for publicly available genotype data (eg. 1000 Genomes or HapMap) that also has associated phenotypes (any traits). I'm wanting to use it as a test run for a GWAS pipeline. Does anyone ...
-1
votes
0answers
41 views

Teaching oneself bioinformatics

I'm interested in understanding bioinformatics and the field of de-extinction. Is it possible to self-teach oneself this field? I am starting with Gerald Karp's and A. Griffith's textbooks on cell ...
0
votes
0answers
17 views

Convert ICD 9 to ICD 10 in Python

I'd like to convert ICD 9 codes to ICD 10 codes in Python. I looked for tools to do this, and I found this one. However, the ICD gets updated regularly and this tool relies on a static mapping from ...
0
votes
1answer
28 views

Where can I get info about A. thaliana proteins' locations?

I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's ...
0
votes
0answers
9 views

How to interpret KEGG's qualifiers in gene list for Cyanidioschyzon merolae?

Looking at the gene descriptions of Cyanidioschyzon merolae's gene in the KEGG REST API, it is not clear to me what some of the qualifying adjectives mean. My understanding is that they have (mostly) ...
1
vote
0answers
35 views

How to split genotypes into two groups from a SNP txt file contains -1, 0 and 1 in R?

I have a SNP file(it is 96 obs. of 1178 variables with -1, 1 and 0 and in some places NA) and I need to calculate Jaccard genetic distance from them in R. Is there any way to convert these 3 values to ...
-2
votes
1answer
43 views

Visualizing top expressed genes

I have a spreadsheet of CPM values I want to visualize the top 20 genes expressed across my samples This is how my data look like ...
2
votes
1answer
49 views

At what point is a gene different between species that we call it a different gene?

I am new to genetics and I know humans share many genes with mice for instance but that there are slight differences in conserved nucleotide sequences. Is there a community consensus around at what ...
0
votes
1answer
27 views

Trinity Multi-species compatibility

I am using Trinity from last couple-up months or so. Initially, using same species in different condition was worked fine for me. Now i am trying to do a DE analysis using multiple species. Actually, ...
-1
votes
0answers
24 views

Graph Neural Network for the Protein Structure Prediction

Does it fit that kind of issues? Say, if I describe resulting protein as a graph since a source amino acid chain has some transition probabilities.
1
vote
1answer
27 views

replacing periods with hyphen

I am a software engineer and not a bioinformatician. I am looking at some code where they are looking at aligned proteins that are in the A2M alignment format (https://compbio.soe.ucsc.edu/a2m-desc....
0
votes
1answer
30 views

What does 'Human Alternative sequence Gene' mean in Ensembl?

I have downloaded a dataset containing RNA-Seq RPKM (reads per kilobase per million) values for 52376 genes (in humans). To find RPKM values for the gene KIR2DL2 in the dataset, I have to search for ...
0
votes
2answers
39 views

HG19 Position meaning

I am looking at genomic data (HG19). I have many SNPs, their chromosomes and positions. I want to look at certain SNP (suppose its chromosome is 1 and position 77,226,919), and extract all SNPs in ...
0
votes
0answers
14 views

Generating intercalation site in DNA for custom sequence

Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
0
votes
1answer
24 views

How to extract part of protein complex separated with HEADER with two molecules from one PDB file

I have a PDB file which contain two molecules (receptor and ligand). Each molecule will have its own header. All in ONE PDB file. ‌The header of receptor section looks like this (line 1-6 of the PDB ...
1
vote
4answers
48 views

Remove gaps from alignment?

I have an MSA (protein sequence) and I have used various programmes (Clustal, Aliview, MEGA11 etc) to align. However, in all programmes I get many gaps which is not ideal as I am trying to construct a ...
1
vote
1answer
50 views

Why does BWA MEM orientation contradict my library prep method

I have some RNA-seq data from a stranded paired end library prep, with dUTP and UDG preparation, so the orientation should be RF (confirmed with sequencing provider). I assembled the reads with ...
0
votes
0answers
17 views

NanoPlot Error : Kaleido Problem

I'm trying to visualize my fastq file using NanoPlot 1.38.1, but it ends up with this error in the log file: ...
1
vote
2answers
26 views

Print first colum is the condition is true using awk

I have a binary file which looks like this, ...
0
votes
1answer
52 views

Help me in understanding the PDB file

Can anybody please explain the below line to me. "We took the structure and coordinates of nogalamycin from the X-ray structure determined in PDB code = 1D17" What do I need to download from ...
1
vote
1answer
22 views

How should I downsample and normalize R1s and R2s and incorporate this into Lexogen's QSPA tool

I am using Lexogen's Quantitative Sequencing Pool Analysis tool (here: https://github.com/Lexogen-Tools/quantseqpool_analysis) to analyze R1 and R2 files. I have been able to successfully run this ...
0
votes
1answer
13 views

how can I get expression of an inserted foreign genes?

hi we have transgenic mice with human gene inserted. if we profom rnaseq for the mice, how can we get the expression value of the human gene inserted to the mice? and use this expression to compare ...
-2
votes
0answers
43 views

How to convert .csv into .vcf file in R

I am working on the annotation of variants and prepared the result in CSV file. I would like to ask you all how to convert xx.csv into xx.vcf file in R ? Thank you
1
vote
1answer
60 views

How do you replace multiple sequence names with new names using python?

I have into a dictionary some sequences. I would like to replace the sequences name for new names contained into a dataframe. ...
0
votes
0answers
36 views

Error in colSums(cts[[i]]) : 'x' must be an array of at least two dimensions

I'm getting an error when creating the counts from a single cell experiment.I'm identifying shared barcodes as well as lowUMI barcodes with the follow code: ...
0
votes
0answers
13 views

Converting miRNA names to miRBase version IDs

I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example: hsa-miR-106a ---> hsa-miR-106a-5p hsa-miR-373* --> hsa-miR-373-5p hsa-miR-33 --> hsa-miR-33a-5p ...
0
votes
0answers
25 views

Basic Docking Work Flow

I'm a computer scientist who is now getting into designing new molecules, with the goal that they dock well to a given target. While I'm used to coding up machine learning algorithms in python, I'm ...
2
votes
0answers
23 views

How to analyze IGV alignment

I'm working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that ...
1
vote
0answers
27 views

What exactly is a reasonable evolutionary criterion? [closed]

I got a rejection of publication which the reviewers mainly point out as not following a reasonable evolutionary criterion for choice of species used for phylogeny creation. In our dataset, a list of ...
1
vote
1answer
39 views

FindMarkers from Seurat returns p values as 0 for highly significant genes

I have been working on FindMarkers function for identifying significant genes in the cluster. But some Significant genes have very low p values, so they are returned as 0 in the output.Any value less ...
1
vote
1answer
31 views

Peptide data visualization

I'm trying to replicate the figure given in this paper using this table which they have given. So what i understand from the figure is they have calculated the zscore between two condition and ...

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