All Questions
6,340
questions
2
votes
1
answer
25
views
Samtools index fails within nextflow workflow but not outside of it
I am a beginner to Nextflow and using it to setup Chipseq workflow and in the workflow below the samtools_index process throws the following error:
...
- 121
0
votes
0
answers
16
views
snRNA-seq analysis: getting NA for certain target genes
I'm doing snRNA-seq analysis of a rare disease. I've gotten upto to finding the markers and getting target genes for a specific protein. However, I'm noticing that a lot of these target genes are ...
- 1
1
vote
0
answers
5
views
How to adjust QIIME DADA2 parameters to avoid eliminating real sequences
I am working with sequence reads (acquired through MiSeq platform by Illumina) from a viral inoculum. I have already used FastP to merge paired-end reads and cut 5' and 3' ends to remove adapters and ...
1
vote
1
answer
43
views
Path value cannot be null error in nextflow
I am trying to learn nextflow and use the process and workflow below to align some Chip seq reads.
For the command below, I am getting the error: ...
- 121
3
votes
1
answer
25
views
16S merging sequences, removes ALL reads
I am currently analysing some 16S (V4 region) rRNA data, using the qiime2 command-line software. Everything is working fine for the most part, until we are to merge the forward and reverse sequences - ...
- 908
2
votes
0
answers
12
views
What is the Manchester style encoding of gene-protein associations
From SBML Level 3 Package: Flux Balance Constraints (`fbc'), page 11
A GeneProduct may, optionally, refer to a Species so as to provide compatibility with the Manchester style encoding of gene-...
1
vote
0
answers
14
views
Results of dn/ds in the branch site gamma model
I am using the BSG model, and I don't understand where are the results for the values of dn/ds for each branch.
Are they supposed to be in the json file (which is a bit complicated to follow) or in ...
- 11
0
votes
0
answers
7
views
Pathway enrichment analysis - minimum amount of proteins?
I have 6 proteins significantly associated with an outcome and have done a pathway enrichment analysis (PEA) with them (in both Enrichr and R with the same outcome). However, I wonder if that is too ...
- 1
0
votes
0
answers
16
views
How to use compareCluster in ClusterProfiler for Multiple GSEA Comparisons in a single GSEA analysis?
I am new to using compareCluster and just want to double check - the input for compareCluster can be ...
- 13
0
votes
0
answers
11
views
PopART (Population Analysis with Reticulate Trees) crashes on Mac Sonoma
Lately, PopART (Population Analysis with Reticulate Trees; https://popart.maths.otago.ac.nz/) causes my 16GB Macbook Pro to run out of memory, despite files being relatively small. I believe it used ...
- 1
1
vote
1
answer
13
views
Nanopore Sequencing with Genotyping and AMR
I have isolates of gram positive and I am interested in Staphylococcus aureus to either do:
Amplicon sequencing using Oxford Nanopore Technology - minion (requiring primers beds and running ...
1
vote
0
answers
18
views
Asterisk wildcard apparently not working for some keywords in PubMed search
For some keywords, adding an asterisk is not increasing as expected but reducing the number of matches in PubMed searches.
I provide here the two issues I have found to date:
The search just for ...
- 133
1
vote
2
answers
50
views
Combing multiple SRA Runs into a single Sample, BioSample or Library
On GEO/SRA some datasets have multiple Runs per Sample, for example this one (96 SRR numbers for 12 BioSample/GEO_Accession/Library Name/Sample Name), and the authors provide their RNA-Seq counts for ...
- 605
1
vote
1
answer
52
views
How can I as a programmer help microbiome research through my programming skills without any specific biology know-how?
I am a chronically ill patient and currently reading 10% human by Alanna Collen. Over the past years, I have become more and more interested in the human microbiome. I am a skilled programmer, but don'...
- 11
0
votes
0
answers
16
views
Best Approach for Translating Aligned Population Sequences to Detect Single Amino Acid Variations?
I have a set of population sequence files that I've already aligned, identifying all existing SNVs (A, C, T, G, del) within each population, while excluding inserts and non-singular deletions.
I now ...
- 249
0
votes
0
answers
12
views
Using CoRAL to reconstruct ecDNA
We are trying to use CoRAL to reconstruct ecDNA. However, we have a problem in CoRAL.py reconstruct, when an error is obtained in infer_breakpoint_graph step. The only difference is reads' article are ...
- 179
0
votes
1
answer
13
views
Nanopore sequencing continuation and data merging
I started a run which should last for 72 hours but unfortunately I had power failure and the remaining hours to complete was 31 hours. However, the base calling and bar coding will be done after the ...
1
vote
0
answers
19
views
Converting GFA to rGFA
I used nf-core/pangenome which created a GFA file. We found panGraphViewer in order to visualize nf-core/pangenome GFA file. However panGraphViewer requires a rGFA. However, it supposed to be able to ...
- 463
-1
votes
0
answers
17
views
Installing Pymol
I was trying to install pymol-open-source and I am unable to run 'python setup.py build install' wherein, after I run this it says 'hexadecimal value 0x0B, is an invalid character. Line 90, position ...
2
votes
1
answer
38
views
How much memory should I allocate to FastQC for analyzing large nanopore sequencing files?
I'm running a bioinformatics pipeline to analyze large nanopore sequencing files using FastQC. However, I keep running into an OutOfMemoryError. Here's what happens:...
- 157
0
votes
0
answers
15
views
How can I visualize WDL workflows?
I would like to graphically visualize my workflow. I tried with Pipeline Builder but I didn't succeed as the http://pb.opensource.epam.com webpage doesn't work.
Thanks!
- 1
1
vote
1
answer
8
views
Troubleshooting E. coli Strain Identification: Identifying Transposon Insertion Sites with Paired-End Illumina Data
I have a problem that needs your help.
I am working on a bacterial genomics project working with E. coli. The lab did illumina sequencing of many strains but I have some problems identifying the WT ...
- 11
2
votes
0
answers
19
views
Extracting RNA reads alignments from a mix of DNA and RNA alignments
I have a fastq file that somehow has a mix of DNA and RNA. It's the sequence data of a DNA sample, but I found one interesting gene that has much higher coverage in exons than in introns. I used STAR ...
- 21
1
vote
1
answer
22
views
Normalizing AMR Gene Read Counts in Metagenomics Data Without Replicates: Is RPKM the Best Approach?
Following up from my previous question, I am currently conducting antimicrobial resistance (AMR) surveillance in water samples using long-read metagenomics (Nanopore sequencing). After analyzing the ...
- 157
3
votes
0
answers
49
views
Improving DNA Sequence Shuffling Code for Speed and Accuracy
I'm working on a Python script that shuffles DNA sequences while preserving their protein-coding potential. My goal is to adjust the codon usage in such a way that the ACGT (adenine, cytosine, guanine,...
- 31
1
vote
1
answer
18
views
Calclation of inbreeding coefficients from pedigrees
Help! I am a complete newbie to cytoscape. I need to use the inbreeding app to compute inbreeding coefficients from pedigrees of pigs which I have as
...
- 11
2
votes
0
answers
18
views
Converting Plink .bed files to .bcf *with* an AC (allele count) field?
I have some extremely large (N ~ 400,000) Plink .bed files that I want to phase using shapeit5.
Shapeit5 requires input data be in .bcf or .vcf format, and that it have an "AC" (allele count)...
- 215
1
vote
0
answers
8
views
How to Visualize ATAC-seq Peaks with Transcription Factor Binding Sites Using IGV
I have a question regarding visualising ATACseq peaks and transcription factor binding sites. I uploaded bigwig files to IGV and I am wondering if there is a way to label transcription factor binding ...
- 11
0
votes
0
answers
9
views
Verification of legal Java version distribution included in Cytoscape install [duplicate]
Our institution is now requiring verification of legal licensing for Java distributions that are included in software installs. Does Cytoscape install include and utilize such licensing with its ...
- 1
0
votes
0
answers
11
views
Demultiplex double hashed cells using Seurat (R)
I am using Seurat to demultiplex my single-cell RNA data, which also has HTO data for hashing. Each cell is hashed once based off it's origin ie organ1, and then hashed based off the cell type ie cell ...
0
votes
1
answer
43
views
Deseq2 model formula and longitudinal experimatal (or time-series) designs
At hand I have RNA expression data of 6 organs from mice with treated and untreated diets, collected at consecutive time points, and I wonder how to design an analysis accordingly in ...
- 3
0
votes
0
answers
9
views
How to fix incorrect file type for Foldseek structurealign?
Using Foldseek with command:
...
Shayan Joarder
0
votes
1
answer
20
views
Finding related Mesh Terms given a substance
Given a list of substance (which can be expressed in any form: general terms or chemical taxonomy) I need to find the specific MeSH term.
I understood that I can use those web services: https://id.nlm....
- 103
1
vote
1
answer
17
views
What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?
MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, raw p-value, -log10 pvalue, Holm-Bonferroni adjusted p-value and the FDR value. And an impact score.
Which value should ...
- 11
0
votes
1
answer
36
views
R function does not return NA when it should
I developed an R function to find a given pattern and check for before and after that pattern, I asked the function to return NA, when the pattern is not found, but now the function returns 0000000 ...
- 115
2
votes
1
answer
29
views
snakefile not able to find files for rule trimming
I am trying to run a snakemake pipeline for small-RNA samples and having problems. The snakefile is given below,
...
1
vote
1
answer
21
views
Differential gene expression (aiming to create heatmap) for raw RNAseq count data from different publications - how to?
I'm new to bioinformatics and RNAseq analysis, I'll try my best to explain the question!
I have raw counts RNAseq data from 3 different publications (so 3 different datasets) that all had similar ...
1
vote
1
answer
14
views
BLAST+ error when running against a custom database: mdb_env_open: The system cannot find the path specified
I am currently attempting to run BLAST+ against a custom database using the following command:
...
- 43
0
votes
0
answers
15
views
How to Choose the Best mRNA Data for miRNA Target Prediction Using psRNATarget: Exons from Assembly vs. Transcriptome Data?
I want to study the target prediction of miRNAs using psRNATarget tool. I have already completed the de novo assembly of this plant genome, and predicted the coding sequences. Now, to perform this ...
- 41
0
votes
0
answers
21
views
10X Cellranger count - Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in
Recently ran three separate single-cell experiments and sequenced them all using the 10X platform. Each of the experiments involved GEX, FBC and VDJ. With the resulting BCL files, csv files with info ...
0
votes
0
answers
7
views
How can I find fasta sequences for gp120 and gp41 for different HIV subtypes?
I need to extract the Env gp120 and gp41 subsequences for the following HIV-1 strains: A, B, C, D, N, and O.
I've been successfully using UniProt for env and tat sequences, but I'm having trouble ...
1
vote
1
answer
42
views
How can I normalize DNAseq nanopore metagenomics data?
I'm working on antimicrobial resistance (AMR) surveillance in treated water samples using nanopore long-read DNA sequencing analysis. After analyzing my data with the KMA tool (a k-mer read alignment ...
- 157
0
votes
0
answers
10
views
How to get Time-Course data for NOS2 & Arg1 Enzymes?
Background: I'm trying to model M1/M2 macrophage switch during a wound-healing process. For a switch from M1 cell population to M2 cell population, there is a reprogramming of the internal metabolic ...
- 1
0
votes
0
answers
8
views
Disabling / Removing / Excluding / Collapsing * Allele SNPs indicating an Overlapping Indel
I am trying to find a way to disable the reporting of Spanning or overlapping deletions (* allele) within the GATK trio genotyping pipeline or a way to properly deal with SNPs given the ...
1
vote
1
answer
33
views
Normalization and Comparison of AMR Gene Tables from Long-Read Metagenomics Data without Spike-In Controls
I am conducting antimicrobial resistance (AMR) surveillance in water samples using long-read metagenomics (Nanopore sequencing). After analyzing the data with KMA (a k-mer read alignment tool, Clausen ...
- 157
1
vote
1
answer
34
views
0
votes
0
answers
18
views
Extracting Snakemake metadata (filenames) with the Snakemake API
I am creating a program that can store all relevant data from a Snakemake analysis run into a gzipped file (or a Pickle, not sure yet), for easy backup and moving around different machines.
To do this,...
- 605
0
votes
1
answer
23
views
Assessing Quality of Error Correction
The main idea:
Given fastq/fasta files containing reads(simulated from ref. genome, with errors introduced) and another file with the ground truth(simulated but without errors) and then the resulting ...
- 1
2
votes
0
answers
17
views
Understanding the Impact of Parameter Adjustment in KMA Aligner for Gene Analysis
I am currently using the KMA aligner (k-mer alignment) from Clausen et al. (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6) to analyze gene sequences (metagenomics) and ...
- 157
0
votes
0
answers
8
views
Verify cell identity
We want to analyze from an article the sequencing data (3 rd generation) of the U2OS line, and we would like to verify if it is that cell line. I was wondering how would be the general procedure, or ...
- 179