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Can't convert my vcf to plink

I have run this and checked the .map for number of contigs and specified in the code "plink --file vcf_corrected --chr-set 897 --make-bed --out output_file but keep getting the error below PLINK ...
Millicent's user avatar
1 vote
0 answers
12 views

Aligners for repetitive sequences

we are interested in detecting repetitive sequences in two cell lines, however, when performing the alignment with pbmm2 on GRh38, not good results are obtained. We are trying to modify the parameters ...
María José's user avatar
1 vote
2 answers
16 views

short Read/percentage threshold for bacterium presence in metagenome

I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
ahmet's user avatar
  • 11
0 votes
1 answer
24 views

"BLASTx for miRNA Annotation: Mature vs. Primary miRNAs as Query Sequences"

I am doing miRNA annotation of a plant genome. I have two files - one containing all the predicted mature miRNAs and another containing all the predicted primary miRNAs. I want to find out which are ...
learnwithscholar's user avatar
0 votes
1 answer
22 views

Normalization in Sequence Analysis Research

I am currently engaged in a research project that involves sequence analysis, utilizing nanopore sequencing and KMA alignment software (k-mer alignment). As I delve deeper into my research, I am faced ...
dim's user avatar
  • 1
0 votes
0 answers
12 views

Guidance Required on Prioritizing Columns for Gene Expression Analysis Using KMA Tool

I am currently in the process of comparing two distinct sets of genes that have been sequenced under two different conditions. My objective is to ascertain whether the expression of specific genes in ...
dim's user avatar
  • 1
1 vote
1 answer
16 views

Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank

Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank(https://www.rcsb.org/). Or is there a way to extract the data programaticaly ...
BadCoder's user avatar
2 votes
1 answer
14 views

How can I search globular proteins by residue count in the RCSB databse?

I want to find some globular proteins with some of the longest individual chains that have all three types of secondary structures,, namely helix, sheet, and loop. So, I tried the following search: ...
user366312's user avatar
4 votes
1 answer
23 views

Protein atlas rna-seq vs protein expression region missmatch

I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in ...
Professional Pigeon's user avatar
1 vote
0 answers
58 views

Recent Bioinformatics Graduate Seeking Resources for NGS and Drug Discovery [closed]

I recently graduated with a bachelor's degree in bioinformatics. Unfortunately, the bioinformatics program at my university was limited, and I'm feeling the need to expand my knowledge in specific ...
MFG's user avatar
  • 11
2 votes
3 answers
33 views

Best practices for handling single-end and paired-end data in a Snakemake pipeline

I am fairly new to Snakemake and am building an NGS data processing pipeline to align ChIP-seq data and call peaks on it, plus some other analyses. The data can be single-end or paired-end, depending ...
Whitehot's user avatar
  • 402
0 votes
1 answer
9 views

StringApp installed on Cytoscape, But does not added to IMPORT/Network from Public Database

I have different versions of Cytoscape in different PCs. one is 3.10.1 and the other is 3.10.2. for both I installed StringApp but in 3.10.2, It is not added to "import/network from public DB&...
Alireza Ebadi Tabrizi's user avatar
0 votes
0 answers
11 views

Problems with pbmm2 alignment after subsampling

I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,...
María José's user avatar
3 votes
1 answer
32 views

Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe

I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
Harry Matthews's user avatar
1 vote
1 answer
27 views

PCA of bulk RNA-seq doesn't show clustering and show large variation in general

I am very new to analyzing RNAseq and I am in a group with very little experience in this regard and I am looking for some advice. My PCA after performing DESEQ2 analysis on my dataset doesn't show ...
NotmyName's user avatar
1 vote
1 answer
39 views

how to see pacbio reads in IGV

This question has also been asked on Biostars I recently used pbmm2 to align my reads to the reference genome, when I specified --sort option it is generated a file with extension bam.bai. Afterwards,...
María José's user avatar
1 vote
1 answer
18 views

Where to obtain fastq_illumina_filter

I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down. Is there ...
Whitehot's user avatar
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1 vote
1 answer
42 views

Indexing the reference genome my process is killed

I am trying to use pbmm2 to create a reference genome index. I'm on a cluster server, I don't know if that's the reason why it has been killed. ...
María José's user avatar
3 votes
2 answers
51 views

Issues with adapter trimming (Trim Galore)

I am new to coding and especially new to bioinformatics so I am sorry if this is a dumb question. Nevertheless, I am attempting to run Trim Galore! to trim my paired RNAseq data, there are no error ...
tphinney's user avatar
1 vote
0 answers
39 views

How much should the 5' adapter and i7 sequence differ?

In a multiome (RNA and ATAC) project I'm working on we chanced upon a strange situation. We're not sure if it poses a problem or not and would like to know if and where I can look it up if necessary. ...
Assa Yeroslaviz's user avatar
3 votes
1 answer
26 views

Fixation index calculation from the vcf files

I used the Python script FSTest (https://github.com/similab/FSTest) for the calculation of the fixation index from the extracted SNPs. I used the following command: ...
DJI's user avatar
  • 31
1 vote
1 answer
35 views

Area under the curve at each time point

I have two variables measured for thousands of patients. One is time to event (with competiting risk), the covariate is severety of a variable measured every 5 seconds or so (variable time steps). I ...
Brigitte's user avatar
  • 111
0 votes
0 answers
17 views

Why don't we use a multivariate (all genes) model for differential expression analysis?

Why differential gene expression analysis (counts) is done with multiple simple models, each with one single gene? Why not one multivariate model with all genes simultaneously? I mean a linear model ...
skan's user avatar
  • 101
4 votes
2 answers
50 views

Converting Gene Symbols to Entrez ID in ambiguous cases

Context: I am trying to perform GSEA GO analysis using data from the GeoMx Digital Spatial Profiler. The GeoMx DSP looks at the expression of a panel of mRNA transcripts using a set of detection ...
J_BioE_'s user avatar
  • 41
2 votes
0 answers
13 views

How do I mount resource directories into my docker image via Cromwell / WDL?

Problem is that the docker image i am trying to run requires a mount points to several resources in order to run. Example: ...
bio-X's user avatar
  • 21
1 vote
0 answers
15 views

Binning then assembling sequencing reads

I am attempting to do something similar to the "Phylomapping" pipeline described in this paper: https://www.nature.com/articles/s41559-019-0914-2. I have sets of Illumina PE reads, that I ...
JohnDoe23's user avatar
2 votes
1 answer
21 views

In snakemake, get input from output, after an expand

I tink I'm almost there, but the input functions are still not working. ...
gl00ten's user avatar
  • 269
1 vote
0 answers
17 views

How to know protomter position in the chromosome?

Could you tell me how to find the promoter position of a gene in the chromosome? Recently I did ATAC-seq expriment and got the result, showing that the peaks related to some genes is assigned to "...
Yeping Sun 's user avatar
2 votes
2 answers
34 views

Where can I get hg38 Copy number Variation (CNV) file?

I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website. Although, I got a link that is not working: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/...
Deb's user avatar
  • 289
4 votes
1 answer
69 views

Replicating VCF Filtering & Trait-Based SNP Extraction Workflow

I'm new to handling SNP genotyping data in VCF format. My goal is to identify significant SNPs linked to a specific trait (like "height") for specific samples in a multi-sample VCF file. My ...
web's user avatar
  • 71
0 votes
0 answers
21 views

Is there any technique that I can use to achieve the required computation without reading all 10 million rows?

I have a data file from a Monte Carlo simulation of fifteen protein chains. The file contains 10 million r_end_to_end 3D vectors as rows and 3 x 15 = 45 columns. My ...
user366312's user avatar
2 votes
2 answers
50 views

Python/R/bash script to ease the comparison of different protein complexes in PDB

I would like to create a table of comparison among similar protein complexes from the pdb. This would be based on their numbers of proteins and the presence of each protein. Is there any way like ...
BioTL's user avatar
  • 31
2 votes
2 answers
27 views

true depth per gvcf location instead of min depth per gvcf block

I am using deepvariant to calls variants on my (WES) data. I am outputting a gvcf file. I am wondering (I cannot find anything in the documentation) how it would be possible to get the true depth per ...
Dandelion's user avatar
  • 353
0 votes
1 answer
27 views

getGEO not working

...
Fatma El-Shaf'ey's user avatar
2 votes
2 answers
52 views

Reasons for extremely low number of DESeq identified differentially expressed genes after RNAseq?

I am fairly new at RNA-sequencing analysis, but I have attempted to analyse the data I obtained from RNA sequencing on my own by following an online EdX class and by basing the majority of the ...
Adrianna V's user avatar
3 votes
1 answer
64 views

RNA-seq QC and alignment error in script

I am analyzing bulk RNA-seq data for Paired-End. I have separate scripts for fastqc, STAR & qualimap but want to run them in a single script which looks like this USAGE: sh rna-qc.sh <path/to/...
S_Malik's user avatar
  • 61
3 votes
1 answer
49 views

BLAST Database error: No alias or index file found for nucleotide database

I have created a database and added environment variables, but an "error message" still appears. How can I solve it? ...
Tina's user avatar
  • 31
3 votes
1 answer
26 views

How to convert bed to wig file!

I was wondering how can I convert bed file to wig file. I have several bed files which look like ...
Deb's user avatar
  • 289
1 vote
1 answer
42 views

Low confidence score from alphafold2_multimer_v3

I am running alphafold2_multimer_v3 in ColabPro (A100 40 GB GPU) with the following parameters: ...
CoolButNubeBioinformatician's user avatar
1 vote
1 answer
39 views

Is there any standardized and ready-to-use dataset available online for download regarding protein geometry? [closed]

I want to do ML model training and data analysis for secondary structure prediction. Is there any standardized and ready-to-use dataset available online regarding protein geometry? For example, the ...
user366312's user avatar
1 vote
1 answer
50 views

Differences between Gencode GTF and Ensembl GTF files

I recently switched from RSEM to Salmon for RNAseq data processing. I started in the Ensembl world and wrote a lot of code around their GTF file (for filtering biotypes/normalization lists etc, http://...
Freek's user avatar
  • 573
3 votes
2 answers
61 views

Multi-pattern search in aligned sequences

I am currently working on a bioinformatics problem where I need to lookup and count the location and count of occurences of 4000-ish 5 character long patterns in each sequence of a fasta file of 700GB....
Swathi Subramanyan's user avatar
-1 votes
0 answers
13 views

Is there anything similar to gener expressions in the case of protein chains?

I am trying to apply a gene-expression-related algorithm to protein chains. What is the closest thing that can be extracted from protein PDB files that we can use to prepare a similar table as to gene ...
user366312's user avatar
3 votes
2 answers
72 views

Running multiple sequence using spades.py on an HPC

I am trying to run a batch script to assemble sequences using the spades.py command on HPC. I tested the script with one sequence (1 forward and 1 reverse read) and this worked. I have 100 sequences ...
Lucy Kelly's user avatar
1 vote
1 answer
18 views

time*treatment series with repeated (i.e: NOT independent) sampling of replicates

I am performing the analysis of cell cultures in suspension, untreated(U) and treatment A and B, at t0, t1 and t2, 4 replicates per treatment. The experiment started with 12 cultures, 4U, 4A and 4B, ...
Alfredo Pagliuca's user avatar
2 votes
1 answer
23 views

Calculating 99th Percentile of Fst values for SNPs within gene

I used SNP data and calculated Fst using the Popgenome R package to identify SNPs that have diverged between bacterial populations. Afterwards, I want to calculate the 99th percentile (P99) of Fst ...
uri's user avatar
  • 85
2 votes
1 answer
62 views

Extract gene sequences from isolates

I have 500 M.Bovis isolates and I want to extract the rpoB and katG genes from these sequences. I took the nucleotide sequences from NCBI and saved them as a fasta file, and then tried to blast for ...
user142632's user avatar
1 vote
0 answers
26 views

Assessing the quality of an assembly

I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda....
thole's user avatar
  • 153
1 vote
2 answers
39 views

Are there efficient tools for PANGENOMES visualization (GFA size >2GB)?

I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most ...
AIsaac's user avatar
  • 21
0 votes
1 answer
46 views

Novogene sequencing archives

We have recently received the sequencing files from this company. For each sample, two files with extension Bam and bam.pbi are available. I would like to ask what is the meaning of the numbers behind ...
María José's user avatar

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