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12 views

Get frequency of index sequences of fastq file

I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
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0answers
17 views

How can I extract sequences from FASTA file using OTUs ID?

I have one FASTA file with sequences and headers, and one OTUs table. What I want to do is replace the current headers in the FASTA file with just the OTU IDs from the .txt file. The files look like ...
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0answers
24 views

How to estimate the phenotypic variation explained by top SNPs from a GWAS study?

I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
0
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1answer
28 views

Solutions to reference bias issue

I've recently learned about the reference bias issue - inability to properly map NGS reads in certain genomic regions caused by the fact that our standard genomic references are linear and do not ...
1
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0answers
15 views

Nucleotide Frequency - HOMER?

I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file. Also, ...
3
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2answers
108 views

Calculating most abundant transcript from RNA-Seq data

vcf2maf uses VEP to annotate variants, and I believe selects the default Ensembl transcript to use for annotation. Sometimes the ...
3
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0answers
22 views

How can I use statistics to compare microbial phenotypes?

Note: this question has also been asked on Biostars I am currently trying to create a theoretical argument that a microbe's phenotype can affect gene expression in their host. I have 5 species of ...
1
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1answer
41 views

fastq file format unknown

I have paired-end fastq files some of which seem to be in a weird format (from a collaborator, not a public database). When I cat the file I get what seem to me to ...
2
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1answer
34 views

Get Salmon mapping/alignment summary

With HISAT2, after the alignment of fastq files you get an alignment summary like this: ...
1
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0answers
25 views

How to compare Log2 Fold Change values

I have 5 sets of Log2 Fold Change values pulled off DualSeqDB. Each of the 5 groups corresponds to a different microbial taxon. Within the 5 groups, there are many Log2 Fold Change values, each ...
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1answer
76 views

How to create this function for lapply?

I have two lists of dataframes. List x and list my_list. Each having four dataframes and their names are same for the two lists, ...
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0answers
27 views
0
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0answers
19 views

Alter Sankoff's Algorithm to give all optimal solutions [closed]

I'm trying to find a way to alter the Sankoff's Algorithm so it will trace back all the optimal solutions and not only one. Is it possible?
0
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1answer
23 views

Differentiating molecules based on peptide sequence? How to annotate?

I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
2
votes
1answer
24 views

Annotatation of transposable elements / transposons / SINE sequences in human

I need to annotate human genome with different types of information, amongst them: transposable elements. I read about repeatmasker, but what I understood is that it estimates the probability of a ...
3
votes
1answer
33 views

Imputation of dog genotype

I am an undergrad working on a set of genotype matrix of dogs, it's in csv file format with information on only the each sample as rows, chromosome and its position as columns, and the rest of the ...
1
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1answer
18 views

Alignment to verify plasmid from forward and reverse Sanger sequencing reads

I am analyzing Sanger sequencing data to verify whether or not the correct protein coding sequence was inserted during cloning. For each sample, I have both forward and reverse Sanger sequencing reads ...
1
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0answers
10 views

How can I associate centrality score of genes(vertices) in a GRN with the probabilistic model in terms of cause and effect?

I'm learning to build Bayesian Network Based Modeling of Gene Regulatory Network of Cancerous Cellular Cells. So far, I have learned to form a Bayesian Network based on nature of genes(i.e Functional ...
1
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1answer
22 views

How to make a video of a gromacs .trj file with VMD

I did gmx trjconv on the GROMACS trr file to generate the .xtc file, and then used ...
1
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0answers
17 views

How can I speed up FASTA ssearch output?

I'm trying to predict targets for miRNA sequences, and so far after reading some papers for other tools that do this, I've found that I should be using FASTA's ...
2
votes
1answer
19 views

Is it possible to correct bond order and conectivity problems in an sdf file according to mol2 files?

I was doing a Virtual Screening Search using Pharmer software. The .sdf output file contains a column in mol format and another column with Root Mean Square Deviations. I can see some bond order and ...
0
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1answer
23 views

Biological datasets for polythetic classification

Question: What are some instances of polythetic datasets in biology? In particular, I am looking for a dataset to benchmark a machine learning algorithm optimized via episodic training. On polythetic ...
1
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2answers
27 views

Getting exact mismatch data from multiple sequence alignment

TL;DR Can anyone point me in the direction of a tool that can be used to input different viral substrain reference sequences (fasta) as well as sequence data (fastq/bam/vcf) and find the most likely ...
1
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0answers
5 views

Computing Maximum Agreement Subtree of two unrooted phylogenetic trees with PhyloNet?

I am using PhyloNet to compute the MAST of two unrooted binary phylogenetic trees but I am not getting the output that I should. I think the issue might be with the way I am writing the trees in the ...
0
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1answer
22 views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
1
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1answer
35 views

10bp sliding window quality score

I am having trouble creating a 10 basepair sliding window that goes through seq and trim them all 10 basepairs that have an average quality score (...
0
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1answer
42 views

Base abbreviations other than ACTGU in sequence file

Short question: where can I find what F and J and < and ...
2
votes
1answer
46 views

Shannon's Entropy and DNA

I have been working with Shannon's entropy (SE) and DNA lately, and referring to the formula and concept of SE, I just wondered whether one should in the case of DNA use each nucleotide as having a ...
1
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0answers
44 views

Alignment tools on desktop for peptide alignment sequence and how to make annotations on alignments look presentable?

I have 10 transcripts where I need to do 5 peptide sequence alignments (2 transcripts per alignment). I need to do this in order to indicate which amino acids lead to which domains. My questions are ...
1
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2answers
18 views

Problems about value log2(IP/Input) less than zero in ChIP-seq?

I have a question about the normalization for ChIP-seq. I used CPM to normalize my bam files of each IP and Input. Then I calculate the coverage of gene bodies for all genes on the genome. I have WT ...
2
votes
2answers
43 views

DESeq2 multiple treatments, multiple time points, multiple cell lines

Note: this question has also been asked on Bioconductor Support I know there are a lot of questions asking similar things here on this forum and I checked the vingette and did a lot of other research ...
1
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0answers
18 views

Convert genbank file into tbl file [closed]

I want to submit some phage sequences to NCBI. So I want to transform a genbank file into a tbl file. Can someone help me please? Thanks
3
votes
1answer
34 views

Finding 2000 bp sequences that occur more than once in the genome

I am looking for a software that can identify long sequences (1500-2000 bp) that occur more than once in my genome of interest. A k-mer counter like KMC could have worked, but KMC has a max limit of ...
1
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0answers
14 views

Bioconductor, genefilter() returns NULL dimensions, is my filtering process wrong?

I'm using R and bioconductor in order to conduct some gene analysis on an Affymetrix dataset (GSE173360) but I'm having trouble at filtering genes. I'm trying to create a dataset called small.eset by ...
3
votes
1answer
64 views

Use Htslib to extract specific region of vcf file

I am working in c++ using the htslib library to parse different vcf files as well as fasta files. My goal is to read in a specific region from a fastafile and then extract all the VCF sites within ...
2
votes
2answers
35 views

Calling for one specific SNP from multiple sequencing runs

Just learning the basics of bioinformatics and bash shell scripting. Is there a correct way to search for a specific allele with one or even multiple sequencing runs? I am searching for prevalence of ...
2
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0answers
38 views

How is the odds ratio of disease risk conferred by a 1-standard deviation increase in PRS calculated?

I am trying to understand how the odds ratio of a 1-standard deviation increase in a polygenic risk score is calculated. I know that this is a commonly used metric of performance of a polygenic risk ...
2
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0answers
18 views

Finding targets genes of putative transcription factor after homer motif enrichment

Steps I have done I have two cell types to compare one is stem cell and leukemic stem cell Two sets of data for each condition RNA seq and ATAC seq. Did differential expression as well as ...
1
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1answer
29 views

How to detect bedtools version used by pybedtools (in order to correctly preserve strand information when merging gtf records)

I have issues working with pybedtools due to strand information being lost after extracting and merging transcript coordinates from a gtf file. It seems that the solution to preserve strand ...
0
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0answers
20 views

How to decide between standardized mean difference (SMD) and log2fold change (log2FC) before doing meta-analysis?

I want to do meta-analysis of alpha diversity between test and control groups across 10 different populations. I want to see what is the summed effect (pool effect) of intervention between the two ...
2
votes
0answers
28 views

Parse RNA variant effect annotations (“r.” format)

I've got annotations for splicing variants in a format like this (this is one variant): Variant: NM_004092.3:c.88+5G>A Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23) I want to extract ...
1
vote
1answer
42 views

What is the meaning of split read?

I want to use rna seq data to later perform functional tests on fusion genes. so before that I need to filter the "best results" (of rnaseq) for deciding which candidates I actually want to ...
2
votes
0answers
9 views

What are the best practices for comparing .seg copy number outputs from iChorCNA to VisCapCancer?

I have shallow whole genome sequence data that I used the tool iChorCNA to find the mean copy number segmentation per region. The tool produces a seg file and can be seen here: https://github.com/...
3
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0answers
28 views

Convert .smp from CDD into HMM file

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
0
votes
1answer
17 views

Modeling number of reads mapped to a gene

I am looking for a probability distribution of a number of reads mapped to a particular gene in metagenomic sequencing (NGS, shotgun, likely illumina). Naively one could model it via a binomial (or ...
2
votes
1answer
66 views

How do I plot clusters based on DNA sequence alignment?

I have a group of about 1050 sequences that have been aligned using blastn. I am now trying to create a cluster plot of the sequences in order to identify similar sequences, something like this: ...
2
votes
2answers
36 views

Why Do I Get Different Results Each Time From AutoDock Vina?

I just tried to use Vina for calculating binding affinity. I used the same protein, the same ligand, the same options, but there are different results. Why do I get different results? Is it the limit ...
2
votes
1answer
36 views

How to know if ID correspond to nucleotide sequence or protein with a script

I have a text file that contains a list of IDs (314 sequences): AVP78031.1 AVP78042.1 ATO98108.1 ATO98120.1 ATO98132.1 ... My goal is to make a script (maybe using ...
0
votes
1answer
37 views

What are common ways to calculate gene length for TPM calculations? [duplicate]

I am aware of this similar question. But the accepted answer there answers how to calculate TPM given a mapping from gene name to gene length. My question is, given an annotation file of genes (for ...
1
vote
1answer
35 views

How to increase the size of the shapes that denotes effect sizes of different datasets and metaanalysis?

I am doing metaanalysis with forestplot from ggforestplot package. I have 7 different datasets from 7 different countries. After metaanalysis, I have 7 Effect sizes and a Meta-analysis effect size, i....

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