All Questions
5,923
questions
0
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1
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7
views
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?
0
votes
0
answers
5
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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 ...
- 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 ...
- 151
1
vote
1
answer
26
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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 ...
- 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:
...
- 19
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 ...
- 111
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votes
0
answers
5
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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 ...
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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 ...
- 101
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votes
1
answer
61
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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 ...
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 ...
- 111
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votes
0
answers
29
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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 ...
- 101
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 ...
- 295
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 ...
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".
...
- 11
-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
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 ...
- 11
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?
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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 ...
- 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 ...
- 513
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:
...
- 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 ...
- 11
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. ...
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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 ...
- 21
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:
...
- 101
0
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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 ...
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 ...
- 21
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 (...
- 393
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 ...
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 ...
- 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'...
- 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 ...
- 21
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.
...
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-1
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0
answers
32
views
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 ...
- 321
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 ...
1
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0
answers
30
views
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 ...
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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 ...
- 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 ...
- 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,...
- 93
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 ...
- 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 ...
- 75
0
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0
answers
19
views
0
votes
0
answers
21
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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 ...
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 ...
- 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.
...
- 393
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...
...
- 188
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 (...
- 393
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:
...
- 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 ...
- 301