Biostar

5,180 results • Page 1 of 104

gene_name in gene_info.items(): region = f'{gene_id}' command = f'samtools depth -r {region} {bam_file}' result = subprocess.run(command, shell=True, capture_output=True, text=True) if result.returncode

linux WGS Bioinformatics SARS CoV2

updated 18 hours ago • Adyasha

recode I get the error > Variant 'ARS-BFGL-BAC-25195' in .lgen file has 3+ different alleles. I am using the most recent version of plink 1.9 (not 2.0 because it does not have the -lfile flag yet). I have searched and...searched and can not find a fix to this. One post suggested filtering out the one with 3+ alleles in their own file, but I could not make that work. Any help would b…

PLINK lgen ped

updated 22 hours ago • Emilie

for allele specific PCR I designed the forward primers for amplification of normal allele and for mutant allele and reverse...allele but what I did was I designed the primers in such a manner that the forward primer began like from the beginning of the

PCR laboratory molecularbiology genetics bioinformatics

updated 2 days ago • beshka194

GenTrain Score, SNP, ILMN Strand, Customer Strand, and NormID. Additionally, I have a file with allele information, including columns for SNP Name, Sample ID, Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2 - Top, Allele1...sample groups, such as treated versus control etc. What should be the optimal GC score cutoff, which alleles should be compared, and how should I conduct these an…

Association Allele Parentage SNP

updated 2 days ago • drajangirija

plink --bfile {my_bfile} --freqx --out {my_bfile} Originally I was just going to see which alleles have higher allele count, but then I see in the plink docs ("For alleles that have exactly 0.50 minor allele frequency...then which allele is labelled as minor will depend on which was first encountered in the PED file.") I am really hoping I dont have to extract...convert to ped, then figure out …

plink

updated 3 days ago • curious

a question about why does gene length effect the normalisation. I understand that the sequencing depth influence the normalisation, so we need to remove the influence of sequencing depth. Many tutorials have mentioned

RNA-seq CPM sequencing

updated 4 days ago • Chen

reads can be just summed up. Doing this will result in the commonly present probes with more read depth, and the unique probes processed just like it would normally be. What is preventing us from doing this and using the resulting

Microarray DNA EPIC 450K Methylation

updated 5 days ago • James

Hi, I finished my imputation on the michigan server and this was the plot from the QC report. Do I need to redo the imputation or does this just indicate that the alleles are flipped? The R2 looks good though, maybe I am just unsure on reading this plot Thanks for any advice! ![enter image description...the plot from the QC report. Do I need to redo the imputation or does this just indicate t…

michigan-imputation-server quality-control

updated 7 days ago • kl

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit [links here](/herald/). This edition of the Herald was brought to you by contribution from [Istvan Albert](https://www.biostars.org/u/2/), and was edited by [Istvan Albert](https://www.biostars.org/u/2/)…

herald

updated 7 days ago • Biostar

I am looking for a [CTO/founding engineer role][1] to join [Voyant Bio][2]. At Voyant Bio, we are on a mission to revolutionize drug discovery with an AI-native data analytics platform. A key challenge in drug discovery is making sense of multi-modal datasets and extracting biologically meaningful conclusions. Our platform aims to build best-in-class data analysis workflows to answer complex b…

engineer

updated 11 days ago • Assaf

n_ref_count = col_logical(), n_alt_count = col_logical(), all_effects = col_character(), Allele = col_character(), Gene = col_character(), Feature = col_character(), Feature_type = col_character(), One_Consequence = col_character

TCGA GDCprepare

updated 12 days ago • glaciya2018

challenges and harnessing the opportunities presented by these advancements, we provide an in-depth exploration of the crucial factors influencing the selection of optimal strategies for achieving robust and insightful

herald

updated 13 days ago • Biostar

but with the new reference give me this error: [.......] WARNING: Reference allele G at 7:116412043 doesn't match A (flanking bps: CAC) from reference FASTA: /home/victor/.vep/homo_sapiens/111_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

vcf vcf2maf maf maftools VEP

updated 14 days ago • Javier

out samples with missingness (% of snps with missing data) above 10% - filter out snps with minor allele frequency (frequency of the less represented allele) below 5% This resulted in roughly 500 samples kept and 1500 snps...figure (AB: pilot samples, CDEF: other samples). My questions are: - Can a differential sequencing depth cause an increase/decrease of heterozygous call in radseq? Is ther…

radseq batch-effect SNP

updated 18 days ago • oselm

I read in one paper they excluded (SNVs) with A/T or G/C alleles to avoid strand issues. What does this even mean? Why would there be "strand issues"? Thanks for your help

quality-control SNV QC SNP

updated 18 days ago • _quantum_girl_

and evaluate ABMs tailored to your research and teaching needs. Here's what you can expect: * In-depth instruction in ABM principles and practice * Hands-on tutorials and exercises using NetLogo, a leading ABM software

Netlogo Individual-Based-Models Agent-Based-Models

updated 18 days ago • carlopecoraro2

In the field of DNA methylation, a diverse array of methods, each with its unique strengths and limitations are available. The working principles of each of the sequencing techniques are quickly discussed below. **1 WGBS (Whole Genome Bisulfite Sequencing)** WGBS involves treating DNA with bisulfite, transforming unmethylated cytosines (C) to Uracils (U). Subsequent PCR converts U to adenine (…

WGBS RRBS

updated 18 days ago • Novogene

How would one determine how much of an association is due to batch effect and how much due to actual allele frequency differences in both cohorts. Any suggestions or advice are highly appreciated. Thank you

Batch-effect omniexpress GWAS GSA

updated 19 days ago • saksis.rihards

finnGen MARKER rsids WEIGHT N ALLELE alt ref EFFECT beta PVAL pval STDERR sebeta FREQ af_alt PROCESS /home/data3/wwh/meta_analysis/metal/input_file/EC...finnGen_ec.txt #FUSCC MARKER rsid WEIGHT N ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE EFFECT BETA PVAL P STDERR SE PROCESS /home/data3/wwh/meta_analysis/metal/input_file...EC/fuscc_ec.txt #UKB MARKER rsid WEIGHT N ALLELE alt ref EFFECT beta_EUR P…

metal

updated 19 days ago • 22211020193

I have made a heatscatter plot in R (I am new to R) and it looks good but I would like to add a Key to label what the colours represent (datapoint depth). This would be a really good feature to help the reader of the figure to understand what it means quickly but I cannot see...to R) and it looks good but I would like to add a Key to label what the colours represent (datapoint depth). This would …

heatscatter visualization R

updated 20 days ago • james.lloyd

I'm interested in comparing single cell RNAseq experiments. RNAseq experiments are often normalized by some kind of global scaling scheme - each cell transcriptome is normalized by some scalar that has been calculated based on various factors - endogenous mRNA levels, capture + RT efficiency, dilution factor, amplification and read depth. I want to compare between different scRNAseq experiments p…

global-scaling single-cell scRNA-seq batch-effect

updated 20 days ago • jmah

Hi there, After having read the vignette, I am really keen to understand in depth how the Limma functions 'removebatcheffect' actually works. Looked at the function: ```r # removeBatchEffect.R # A refinement

limma RNA-Seq batch-effect

updated 21 days ago • Mozart

from the Mexico City Prospective Study (MCPS). This includes genome locations, population specific allele frequencies, alleles and annotations for 142 million variants. submitted by: [zx8754](https://www.biostars.org/u/3919

herald

updated 21 days ago • Biostar

if the base in the reference is C and there are two transcripts TrX and TrY and two alternative allele A and T, with this option VEP chose first the best transcript (e.g. Tx) and then the allele that generate the worst outcome...on that transcript (e.g. A). I wonder, in case of "similar" outcome by the two different alleles (e.g. they cause both a missense mutation), if the Allele Frequency is…

VEP

updated 24 days ago • atariw

Hello, Is it important to filter variants based on the Allele Count in genotypes for each ALT allele (INFO/AC)? Should I always, by default, set this value to a minimum of 1 (using bcftools

vcf bcftools

updated 25 days ago • maevalefeuvre

way to downsample nanopore long-reads. Ideally I would want to downsample to a specific average read depth e.g. 5x I have found a few methods e.g. using `samtools` but this seems to work for downsampling to a specific number or fraction...of reads. `Rasusa` downsamples to a specific coverage /depth but requires fastq input and I would prefer to downsample my BAM files so I don't have to re-ru…

nanopore BAM QC ONT downsampling

updated 26 days ago • eesiribloom

from different sources, I've noticed that variants with the same chromosome, position, reference allele, and alternative allele sometimes have different rsIDs. Why is this the case, and which rsID should I use? 1. Initially...I had obtained from Ensembl-VEP, even for variants with the same chromosome, position, reference allele, and alternative allele. 3. The data from the other study I want to …

UKB rsID UKB-PPP ensembl-vep dbsnp

updated 26 days ago • lsy9

in adaptive sampling, I though we could discard telomeres and centromeres in the calculation of read depth for then assessing copy number. My first question is if this is a good approach. The second thing is that I already have

T2T Nanopore AdaptiveSampling aneuploidy centromeres

updated 27 days ago • njornet

genotype information for a particular site AND a particular sample that did not reach enough read depth. - Filter high coverage I want to filter genotypes (not samples, not sites) that have a DP above the 99th percentile within

filter vcf coverage

updated 27 days ago • MBarcelo

Hello, Has anyone come across the below results in vcf with both alleles as wild type and variant. I am not sure where to start checking. Any thoughts ``` Chr Start End Ref Alt chr9 127447499 127447499

whole-exome variant-calling

updated 28 days ago • priya.bmg

genotype ~3000 SNPs from amplicon sequencing data, using `--genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles $vcf --output_mode EMIT_ALL_SITES` mode. However, it take huge time to call these variants, ~20h. And I found that adding

HaplotypeCaller GATK

updated 4 weeks ago • J.F.Jiang

I am trying to calculate the depth coverage between short read and long read in rna-seq. Below screenshot is the output file, [prefix]_Log.final.out. My...I am trying to calculate the depth coverage between short read and long read in rna-seq. Below screenshot is the output file, [prefix]_Log.final.out. My understanding

rna-seq short-read long-read

updated 4 weeks ago • shinyjj

RNA-seq, scRNA-seq, proteomics data etc) to identify neurodegenerative disease target - Conduct in-depth computational validation using sophisticated in silico data and models. - Analyze and compile crucial datasets, contributing

intern

updated 4 weeks ago • Shicheng Guo

3. How should one address potential technical factors such as preprocessing issues, sequencing depth, or sample preparation that might influence the identification of such cell populations? P.S. Batch effect corrections

Transcriptomics Single-Cell

updated 4 weeks ago • Daddy

of VH genes only and 2x250 bp NovaSeq runs worked really nicely, giving us the coverage and depth that we needed especially in the early rounds of selection when diversity is still high. However, this new library contains...inserts of about 800-900 bp and I don't know how to go about sequencing it. The read depth is super important for calculating the fold-enrichment during selection. The linke…

Long-read phage NGS

updated 4 weeks ago • Ryan

are a lot of soft clipped bases to the left and to the right of the detected CNV (found due to read depth). Do the soft-clipped reads indicate the breakpoints of the amplicon? If so do these soft clipped bases align to the amplicon

long-reads IGV ONT

updated 4 weeks ago • Kay

I am using Freebayes (v1.3.6) for SNP calling analysis on eggplant population data. While scrutinizing the VCF file, it has come to my attention the heterozygous assignation in some cases. This was the command used to perform the SNP calling: /usr/bin/freebayes -b all_parents_mapped_BWA_v3_20X_dedup.bam -f /data/users/vbarfon/Genomes/Solgenomics_2019_08_30/Eggplant_V3_Chromosomes.fa -v multithre…

depth freebayes heterozygous genotype

updated 4 weeks ago • viir.caraja

output-file svHyGen/candidateSV.0000.vcf --tumor-output-file svHyGen/tumorSV.0000.vcf --chrom-depth chromDepth.txt --edge-runtime-log svHyGen/edgeRuntimeLog.0000.txt --edge-stats-log results/stats/svCandidateGenerationStats.xml

manta gdb

updated 4 weeks ago • Greg

Subject: Seeking R/Python Script for Allele Frequency among multiple population Data Collection from gnomAD Message: Hello everyone, I'm in search of R or Python...script capable of fetching allele frequency data for a batch of SNPs from the gnomAD database, encompassing all populations. Ideally, this script would...accept SNP IDs as input and output a data frame containing the allele frequency…

gnomAD

updated 4 weeks ago • Shicheng Guo

vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Allele*; _Alloc = std::allocator <allele*>; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed...Aborted (core dumped)**</allele

freebayes

updated 4 weeks ago • emilydolivo97

Hi there I have several individual VCF files on which I'm working on to retain calls with only a depth greater than 10 and a genotype quality greater than 30. Also, I'm preserving missing sites. However, I wonder if there is

conditions vcf filters bcftools

updated 4 weeks ago • Matteo Ungaro

Hi all, I've previously called variants from WGS data but am now tasked with using single-end ddRAD-seq data. It seems STACKS is popular for this purpose, but I'm confused by how it handles the high levels of read duplication that seem inherent to RAD-seq. The only reference to duplicates in the manual here https://catchenlab.life.illinois.edu/stacks/manual/ is a code snippet that says: &g…

PCR VCF STACKS RAD-seq

updated 4 weeks ago • maxrwjones

FASTA and one or multiple alignment BAM as input, and outputs a multi-sample VCF along with allele counts: Submitter's note: countless times, you just want to know what the alleles are at a position; the task is surprisingly

herald

updated 4 weeks ago • Biostar

the location of the first column chr10:11974892 belongs to a unannotated region and the alternative allele MTHF1L. So I am not sure what gene to attribute this variant to. Additionally I noticed that the reference that for many...the SVLEN field is 0 meaning there is no difference in length between the reference and alternate alleles. I do not quite understand what the entry is telling me in that…

manta Variant-calling VEP

updated 4 weeks ago • josh.mannheimer

Quality Control Calculating QC Statistics Statistics: Alternative allele frequency > 0.5 sites: 49,935 Reference Overlap: 64.83 % Match: 62,365 Allele switch: 0 Strand flip: 0 Strand flip and allele...switch: 0 A/T, C/G genotypes: 0 Filtered sites: Filter flag set: 0 Invalid alleles: 17,968 Multiallelic sites: 3,775 Duplicat…

Michigan-Server Phasing TopMed

updated 4 weeks ago • berndmann

perform meta-analysis of GWAS, but one of the public summary data I downloaded did not have effect allele frequency. I am wondering if i can perform METAl without effect allele frequency or is there anything I can do to fix

allele-frequency gwas

updated 4 weeks ago • 晗颖

I have run superFreq on a couple of samples from gallbladder tissues along with OCUG and NOZ cell-line which have ERBB2 amplifications. The combined CNA heatmap that lists out the calls gene-wise can call the amplifications in these samples, but the tsv file stating the M statistic, defined as, "Consensus Log2 fold change of read depth with respect to the reference normals across the segment, no…

rna-seq Superfreq cnv

updated 4 weeks ago • aksh

databases and build my own (snpEff), however, in both cases, not all my variants are annotated with Allele Frequency (AF). The problem is: those variants not annotated in VCF has Alelle Frequency in dbSNP (ncbi website). I tried

Variant-Calling WGS Alignment

updated 4 weeks ago • Luiz

a database for these two similar datasets. I realise most of the additional proteins will be alleles of annotated genes. This is just a test dataset for a later larger project. Regardless, is there a way to download all

ncbi

updated 4 weeks ago • dthorbur

PL values at LK031787:1508, cannot merge. The tag is defined as Number=G, but found 5 values and 2 alleles.** This is what I have in position 1508: ![enter image description here][1] Whereas my comment section includes following

vcf bcftools

updated 5 weeks ago • analyst

5,180 results • Page 1 of 104

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