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How can I convert a BED file to GTF/GFF with gene_ids?

Given a .bed (BED12), how can I convert it to GTF/GFF formats with gene_id attributes? What is the fastest way or available tools to do it?
Alejandro Gonzales-Irribarren's user avatar
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0 answers
5 views

How to identify phages from Phaster in PhageDB

I am running searches for genes using Phaster and would like to look up the phages that have them on PhageDB to learn more about their distribution. The blast search returns a lot of information about ...
Amy's user avatar
  • 1
1 vote
0 answers
8 views

MMSeqs taxonomy running for over a day

I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day. In their paper they claim ...
Rainman's user avatar
  • 151
1 vote
1 answer
26 views

Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index

I'm trying to run RNA-seq on single-end mouse RNA data (50bp reads) but have very limited RAM (<4 gb) - I don't think I really have a way to work around this memory restriction, and wanted to try ...
mz.'s user avatar
  • 11
1 vote
0 answers
77 views

bwa mem hangs after a few thousand reads

I am trying to align a bunch of paired sample fastq files using bwa mem. My original command was: ...
padakpatek's user avatar
1 vote
0 answers
8 views

What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?

Tries are a data structure that can be used to efficiently store and search for strings. Tries created from an ordered sequence of strings differ from the regular Tries in the following way: If there ...
GEP's user avatar
  • 111
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0 answers
5 views

Which molecular interaction (MI) terms refer to dierct binary interaction detection techniques?

I am currently researching protein pairs that engage in direct binary interactions. My primary sources of information are databases such as STRING, where experimental evidence is often annotated with ...
kate allerton's user avatar
0 votes
0 answers
23 views

Generating force-fields for ANY residue

Is this possible to generate force fields for any residue in my .pdb file? I am trying to generate conformations for the proteins with arbitrary residues binded to it from .pdb files using OpenMM, but ...
JaktensTid's user avatar
0 votes
1 answer
61 views

issue with rna seq analysis

I am working on RNA seq analysis and I would like to know the following things: Current Methods: downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 performed ...
subhiksha sundaram's user avatar
1 vote
0 answers
39 views

Energy error margin for protein structures

I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
Omar Shehab's user avatar
0 votes
0 answers
29 views

ERROR IN FUNCOTATOR: [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

I ran the "funcotator" step from the GATK somatic short variant discovery (snvs + indels) pipeline and used the output of filtermutectcalls as input, but ...
Rita Soares's user avatar
0 votes
0 answers
34 views

Generate simulated bam for certain snps

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
Shafayet Rahat's user avatar
1 vote
0 answers
80 views

Eigen phred score interpretation

I need help. I am not able to find any reference for Eigen_phred_coding prediction tools score from dbNSFP. I know that it may be scaled in a similar manner to CADD_phred - ranking raw values from ...
Lukas Chumchal's user avatar
1 vote
1 answer
53 views

stacked barplot with error bars

I need to create a barplot with error bars, my data consists of 2 groups called "Genot", with 3 sub-groups "Suberin" for each, associated with a value "Percent". ...
user18598's user avatar
-1 votes
0 answers
25 views

How can I convert ecat(.v) file to nifti(.nii) file in python?

I want to convert ecat file to nifiti file or ecat file to dicom so I can change it to .nii later. I would like it in python if possible. Do you have any library suggestion? Thank you
user18593's user avatar
1 vote
0 answers
15 views

(Complete) Stuctural Models of Antibodies: Combining Fc and Fab from pdb to Build Hinge Region? Or what?

I'm a newcomer to the field of antibodies, and I'm seeking guidance on obtaining 3D structures for my molecular simulations. After browsing the PDB databank, I noticed that there are Fab and Fc ...
LameSloth's user avatar
2 votes
1 answer
92 views

Where to access the WGCNA tutorial documents: Horvath lab site down

I am currently using the WGCNA package for some analysis and it seems the Horvath lab site is down. Does anyone know of anywhere else I can access the tutorial documents?
Stephanie O'Donoghue's user avatar
0 votes
2 answers
40 views

How long should it take to cluster Uniref?

I have the Uniref90 dataset containing around 76M sequences. I have made modifications to all sequences based on a reduced amino acid alphabet. I am trying to cluster it again at 90% identity. I am ...
GIONII's user avatar
  • 11
0 votes
1 answer
46 views

Are there applications of semi-supervised learning to genomics?

Semi-supervised learning is when a portion of the training data set is labeled, and the rest is unlabeled; the unlabeled data is used to improved learning performance / accuracy. Are there (i.e., have ...
BigMistake's user avatar
2 votes
0 answers
35 views

How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: ...
DN1's user avatar
  • 45
1 vote
1 answer
38 views

Get a certain gene sequence from bam/vcf and reference

I need to get a fasta sequence of a certain gene for a certain worm strain that is different from reference. I have a reference genome, BAM for the strain of interest, and coordinates of the gene. I ...
user98747's user avatar
0 votes
1 answer
44 views

Does AlphaFold actually calculates the fold?

After reading through papers and the code, I'm still not clear if AlphaFold and the likes do actually calculate the 3d structure. My current feeling they are more like information retrieval engines. ...
biocodz's user avatar
1 vote
1 answer
27 views

PANTHER FUNCTIONAL CLASSIFICATION in R

Does anyone know of a way to programmatically get panther protein class terms and IDs for a gene list, in a way that the classification structure is preserved (PARENT CLASS + CHILD CLASS)? i.e. For a ...
ricardo3889's user avatar
1 vote
1 answer
47 views

Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?

I have single cell data which I want to annotate with the seurat package, so I ran this code in R: ...
Rita Soares's user avatar
0 votes
0 answers
13 views

Estimating rate of evolution from a phylogeny

Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species? I was using terminal branch length from a phylogeny and would quite like to try sub ...
Nitara Wijayatilake's user avatar
0 votes
0 answers
8 views

Exporting Panther functional classification of gene list

After inputting a list of gene and running an analysis in https://www.pantherdb.org/ (such as "functional classification"), I get a result table that is limited by an X number of entries ...
ricardo3889's user avatar
0 votes
1 answer
80 views

Statistical approach to link DNA methylation with toxic element exposure and health outcome

I would be thankful to you if you can help with the statistical approach for case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
bioinfonext's user avatar
0 votes
1 answer
23 views

getting NCBI TAXname by R

I have a data frame on R, called qIns8, with 14 columns and 204 rows. the column called "subject tax id" has NCBI taxIDs for the corresponding row, I need a script to add another column to ...
Farzad Beikpour's user avatar
2 votes
2 answers
57 views

Sequence Alignment for sequences with the same length

I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
MirzaK's user avatar
  • 21
1 vote
0 answers
10 views

Producing just network files from BiG-SCAPE

I was wondering if anyone knows off-hand if there is a way to run BiG-SCAPE without producing the svg or html files? All I want is the networking files (which I can play with in CytoScape). There isn'...
Rainman's user avatar
  • 151
2 votes
1 answer
75 views

Mitochondrial genes - TPM calculation bulk RNA-Seq

This question was also asked on Biostars I was wondering if any of you have encountered a situation for bulk RNA-Seq where, possibly due to low sample quality or presence of dead cells, mitochondrial ...
nick_b55's user avatar
3 votes
1 answer
35 views

biomarRT conversion of symbols

I wanted to use the code to convert mouse to human symbol, but I have problem with the mirror, I've tried to establish another one, but continue to have the same problem. ...
María José's user avatar
-1 votes
0 answers
32 views

How to create positive and negative Bar Graph

My Data: ...
Emy Alade's user avatar
2 votes
0 answers
43 views

How to incorporate negative controls in DESeq2

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any "control" data to set as baseline, either from ...
Karthik Nair's user avatar
0 votes
0 answers
59 views

Convert genotyping results to vcf or other plink formats

I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
Alice Yan's user avatar
1 vote
0 answers
30 views

Need help with binding DB API

...
Neeleshwar Pandey's user avatar
1 vote
0 answers
9 views

Identification of metabolites through spectral library search

I am very new to single-cell metabolomics and today I want to jump in this area. I have been reading many review papers related to identification of metabolites at single-cell resolution from spectral ...
Huy Nguyễn's user avatar
1 vote
1 answer
26 views

Confirming Identity of clone in Phylogeny

This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole ...
prekij's user avatar
  • 13
1 vote
1 answer
44 views

Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?

Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
Charles's user avatar
  • 537
0 votes
0 answers
45 views

how to use CIBERSORT

I have seen in several articles, the use of CIBERSORT to calculate the proportion of immune system cells using gene expression data, I would like to try it but I have not found how to install it for R,...
María José's user avatar
2 votes
2 answers
124 views

How to add charges to a PDB file?

I did some calculations using a PDB file as input. As a result, I got a file with the atomic partial charges (only the values in one column, no other information) and the output PDB file structure ...
Camps's user avatar
  • 123
2 votes
2 answers
67 views

What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
Mirko's user avatar
  • 75
0 votes
0 answers
19 views

PyRanges: drop specific record from an object

Given a specific PyRanges object, such as ...
Einar's user avatar
  • 131
0 votes
0 answers
21 views

Unable to access error logs of failed cromwell execution (WDL) in local machine running in ubuntu environment

I was trying to run bases2fastq software downloaded from the element bioscience platform. I was running this software through WDL workflow named list_fastq. For some reason, maybe syntax, my cromwell ...
Jivesh Singh's user avatar
0 votes
0 answers
12 views

Metabolic Modeling

I am trying to identify the flux of IgG antibody in CHO ovary cells with optimised biomass and glucose input ranging from 0 to 10, but I am not sure when I run the FBA analysis what should I define my ...
July's user avatar
  • 1
-2 votes
3 answers
82 views

Filtering columns from large file based on a column list

I have list of samples as a txt file and want to only keep these samples from this large file; column name is samples name in the large file. ...
bioinfonext's user avatar
1 vote
1 answer
28 views

How many Ns and ns in GRCh37 / GRCh38 per 'canonical' chromosome?

This is kind of pedantic, but I'm not sure where to look... For GRCh38 (and a lot of work...) I have the following... ...
Dan Bolser's user avatar
1 vote
1 answer
88 views

Mendelian randomization

I would be thankful to you if you can help with how I can use MR from my case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
bioinfonext's user avatar
0 votes
2 answers
45 views

How to run a GATK Docker Image with local files?

I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command: ...
rimo's user avatar
  • 923
0 votes
1 answer
30 views

VEP annotation INFO field Ensembl IDs and locations

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is ...
Dandelion's user avatar
  • 301

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