Biostar

5,180 results • Page 2 of 104

I've been calculating the depth of coverage this way: number of reads * average read lenght / lenght of the reference genome [Wikipedia][1] shows the same...I've been calculating the depth of coverage this way: number of reads * average read lenght / lenght of the reference genome [Wikipedia][1] shows the same method...I have also been using [Tablet][2] to check my assemblies, and it seem…

depth assembly

updated 5.5 years ago • Jane

Hi everyone, I am performing an allele-specific RNA-seq analysis. Basically, I used SNP positions between two alleles of a mouse hybrid strain to separate...reads specific to each allele. Now I normalized the data, as usual, using Deseq2 function and performed differential expression analysis. However...I wonder if the normalization method for allele-specific counts will be the same or differe…

RNA-Seq allele-specific normalization SNP next-gen

updated 4.7 years ago • Ankit

Hi, I am using samtools to compute depth at a specific region. Here is my code: samtools depth 1.bam 2.bam 3.bam -b 1.bed the bed file is like this: #chrom start end...1 1000 2000 this command output depth at each locus which is not I want. I tried samtools depth 1.bam 2.bam 3.bam -r 1:1000-2000 which output same result. I am really...confused how can I output the average …

WGS

updated 2.9 years ago • lz1903

I have used the samtools coverage function to compute mean depth of coverage for a bam file, and the samtools depth function in conjunction with cat to determine the maximum and minimum...depth of coverage values for this same bam. Oddly, the maximum depth of coverage value from the txt created using samtools depth...is a smaller value than the mean depth of coverage given by samtools coverage. …

samtools depth-of-coverage

updated 10 months ago • rachel.shadoff

Hello all, I'm using samtools in order to get the depth of a file called file.bam, but the output I have is like this: samtools depth file.bam > output.txt 11 88911833 2 11 88911834...sequence, the second column is the base index within the reference, and the third column is the depth of coverage for that base. But I need at the end the read depth represented like 100X, 150…

depth samtools

updated 5.3 years ago • LimMo

Dear community members, I do not work with SNVs directly and I can not check this myself. But I use allele frequencies of SNVs for CNAs calling, so this question is quite important for me too. Saying "allele frequency" I am meaning...the ratio between number of reads supporting alternative allele vs overall read depth coverage of the position. It is well known that allele frequencies of SNVs h…

snv

updated 4.5 years ago • German.M.Demidov

I have several individual sequence data sets with very low average read depth (i.e. < 5) across most sites that cannot be further improved upon with repeated rounds of sequencing. Consequently, I...such as HaplotypeCaller Specifically, even though these are diploid Drosophila genomes, with read depths of 2-3, calling diploid genotypes is too error-prone to pursue. My first thought was …

GATK

updated 2.7 years ago • shpak.max

Greetings all, I am trying to simulate a vector of NGS depth based on mean depth. I do NOT want to simulate reads, just depth. I have tried simulating a random walk, starting at the mean...depth. This captures the autocorrelation of depth across positions, but fails terribly at modeling average depth. Any ideas

reads depth-of-coverage simulation

updated 10.9 years ago • Zev.Kronenberg

sequenced, so I expect to find different snp in a single position. i would like to find the total depth for the position , which i can do using samtools depth, and the depth for each snp (number the times that each variant appears

SNP coverage

updated 6.6 years ago • paumarc

calling method. For a handful of variants, I want to obtain their individual mean MQ, and their raw allele counts. One way would be to use the **samtools mpileup** software, but that will, at some point, be removed and is deprecated...I assume, is the mean from all the BAMs I give it as input. Likewise, I can get the cumulative raw depth (INFO/DP) but not the raw depth (FORMAT/DP) or allele spe…

snp alignment

updated 4.5 years ago • brian.leon-ricardo

I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Here are how these sites looks like: Most of these allele have VAF =1 and reside on the region of...high sequencing depth with relatively poor alignments (seems to be germline variant). My first guess is that they are disgarded by early steps

haplotypecaller vcf

updated 4.6 years ago • CY

is homozygous or heterozygous. For a particular sample, I see a high proportion of the alternate allele (87%) and a lower proportion of the reference allele (13%), yet according to the reference data, this sample is heterozygous...When I pass this data to bcftools, it reports the presence of the allele but as if it were homozygous. Is there a way to simply get the abundance of the alternate and r…

variant-calling bcftools

updated 12 months ago • Fernando

then samtools mpileup to call variants, then shoremap to analyze the variants. I noticed that the allele frequencies of variants given by shoremap convert are much lower than the allele frequencies I can calculate by hand...iDP; } DP4 is information about the number of high quality reads and DP is total read depth. Both of these values are calculated by samtools mpileup and included in t…

shoremap allele-frequency

updated 11 months ago • emilywynn6

I would like to calculate some very general summary statistics on bam files: average read depth and breadth of coverage at >= 1x and >10x. I am using `samtools` and `sambamba` to calculate `depth` and they seem to produce...summary files below. According to the documentation, these are the default filters: - `samtools depth` filters reads that have any of the flags UNMAP, SECOND…

sambamba samtools depth coverage

updated 3.1 years ago • Johannes

labeled as missing that variant. Instead, I want the VCF to show that the sample has the reference allele (safe to assume in my application). Is there a way to call missing variants in a VCF as the reference allele? What tools can...ref-for-missing` flag in `vcf-merge` does of course not give the variants any annotation, like depth and genotype quality

SNP genome VCF

updated 6.6 years ago • olavur

Hi all! I need help, I have files from GBS and need to know your depth of files. I know it is necessary “samtools depth”, but I do not know the difference between using Flags (-a) or not using it. Because

Samtools

updated 12 weeks ago • adriana michelle

Hi, I'm having trouble understanding read depth in vcf's called by `somatic-sniper`. Here is a sample vcf file: ``` ##fileformat=VCFv4.1 ##fileDate=20140428 ##phasing=none ##reference...join="" mode)"="" prior="" quality=""> ##FORMAT=<id=vaq,number=1,type=integer,description="variant allele="" quality"=""> ##FORMAT=<id=bq,number=.,type=integer,description="average base="" quality"=…

somaticsniper vcf variant-calling depth

updated 2.5 years ago • Jordan

Hi, everyone! I want to have a look at the depth of each position in my .bam file, so, the samtools used,samtools depth my.bam, but I find I can't get the output parameter, it...only output in my Terminal screen. I want a file with whole positions' depth. How can I do it? Thx

samtools depth-of-coverage output

updated 11.9 years ago • Chris

How is the nomenclature of an allele derived. For an example the snp in MCPH1 is referred to as G37995C is the G the ancestral allele or is it the derived allele

allele

updated 8.7 years ago • jspencenumber29

Hi All, I have a bam file and I calculated read depth using samtools depth and I now want to filter the bam file to have only the contigs that have a depth between a certain...value. I was able to filter the samtools output to create a txt file that only contains the depth region im looking for, but Im struggling to then filter the bam file with this information. The depth file has three colu…

sam bam filter

updated 2.1 years ago • Dak

Greetings! I would like to study deeply, question about sequencing depth. By sequencing depth I mean - reads per sample, its very important in my experiments. I will be glad to any link about this

16S metagenome depth

updated 2.0 years ago • poltora4enko

example, applying a 10X filter means calculating and providing genomic regions with at least 20 read depth, excluding regions with below 20 read depth, and then providing coverage results. Is there a way to do this using `samtools...depth`, `samtools coverage`, or any other tools

Depth-of-Coverage CRAM WGS

updated 5 weeks ago • prds

Hello dears all, Excuse me I think I have got stuck in a misunderstanding about depth. Could you please let me know what is the difference among depth of coverage (which we take from each sample using samtools

snp next-gen genome vcf sequence

updated 5.2 years ago • jaafari.omid

Hi all, We used multiple PCR to prepare the amplicons and loaded on MiSeq to get the sequencing data. We now want to get the average depth of coverage for targeted amplicon. However, it seems that if the amplicons have overlapped regions, GATK will merge the...the amplicons and loaded on MiSeq to get the sequencing data. We now want to get the average depth of coverage for targeted amplicon. …

coverage depth

updated 17 months ago • jfjiang

Hei everyone, for my project i did capture sequencing of mulitple individuums. Somehow the depth and coverage is not as high as expected. Now i want to plot the output of samtools depth. Unfortunatly i am not able to write...server a histogramm. On the x-axis should be plotted the position in basepairs and on the y-axes the depth. The bins of the x-axis should conclude 1Mbases and at last it w…

plot depth samtools

updated 2.8 years ago • dominik.lagler

Hi everyone, I'm trying to use "mosdepth" in order to get the depth in each position in a bam file i have (of rna-seq data). I tried to run - > mosdepth output_file bam_file and one of the files...i get is: > output_file.per_base.bed.gz When I open this file i see that actually the depth i get is not always per position, but most of the times it is for some preceding positions:…

mosdepth RNA-Seq depth

updated 3.4 years ago • rotemkat

Imagine 10 alleles (A-J), each with a 10% population frequency at one locus. 1. If you know that your sibling had alleles A,B, what are the probabilities...of observing any allele at your position in the pedigree. 2. If your nephew (on your mother's side) has alleles C,D what are the probabilities of observing...any allele at your position in the pedigree. 3. If your nephew (on your mother's sid…

frequencies IBD pedigrees allele

updated 21 months ago • literature.02

Hi Dear all I want to know why we separate multi-alleles Variant from bi-alleles Variant in our analyzes? In other words, why do most researchers in their own analyzes separate...the multi-alleles Variant from the bi-alleles Variant and keep most of the bi-alleles

genetics population

updated 2.8 years ago • mostafarafiepour

IS there a way that samtools depth include gaps? Right now every time I run samtools depth the data just skips the base positions without coverage. Thanks

samtools depth-of-coverage

updated 12.1 years ago • Juliofdiaz

In 10X single cell RNAseq how can be achieve a good sequencing depth to detect lowly expressed genes. Soemthing similar has been shown in this paper https://www.nature.com/articles/nbt.2967...to get a good sequencing depth in a microfluidics system. Is better sequencing depth is possible in micro fluid system and not in 10X genomics? An thoughts

RNA-Seq

updated 3.6 years ago • kanwarjag

I have PE125 sequence data and want to calculate the average read length of my reads. - average length = total yield base/total reads - total yield base = `samtools depth -q 0 -Q 0 my.bam | awk '{total+=\$3};END{print total}'` - total reads also from bam file The result show the average length of my reads is...of my reads. - average length = total yield base/total reads - total yield base…

samtools-depth

updated 24 months ago • Yuu

and I am trying to understand the output of the SNP calling. I can't understand what the mean sample depth is

depth SNP

updated 3.2 years ago • giulia.trauzzi

Hi all, I have a question, How do I determine the depth of coverage in a .bed file in UBUNTU

depth of coverage file .bed

updated 7.9 years ago • wilibaldo

I am struggling with what kind of analysis belongs to allele specific level. What is the exact meaning of allele specific gene expression? If we got bunch of SNPs in some gene, could...we say there are bunch of alleles of this gene? If this is the case, are we always doing the analysis which is allele specific? I am really lost in the concepts...I really want to know what kind of events are calle…

allele

updated 7.9 years ago • Honglang Wang

article: [article][1] In this article, authors mention and I quote **'pathogenic variants with allele frequencies greater than 0.01% were well characterized in publications and included many founder mutations.'** I want...to make if I understand allele frequency correct. Does allele frequency greater than 0.01% means variants for whom the alternative allele count...is greater than 1 so t…

snp allele frequency

updated 2.3 years ago • peter

I am trying to estimate coverage depth for my de novo transcriptome assembly. I used Illumina Hiseq 3000/4000 PE with a PF yield of 140 million clusters. Since...finding the total number of transcripts. Can someone tell me of a way to calculate the coverage depth. Will I have to calculate the coverage depth on average for each transcript or can I get a coverage depth for the entire

RNA-Seq Assembly next-gen rna-seq

updated 5.6 years ago • babji2318

p/67579/ --- **Original Question** I'm doing ChIP-Seq analysis and want the read depth at each and every genome position aligned in a set of bam files, includign 0s for positions covered in one bam file but...not another. Totally raw-no score filtering. Both `depth` and `mpileup` accept a list of bam files. **DEPTH** >Computes the depth at each position or region. >`a -a, -a…

samtools mpileup depth ChIP-Seq reads

updated 7.5 years ago • ariel.balter

how to find the allele frequency? is any online tool is there? allele frequency table for human. most commonly found allele in human

allele frequency

updated 11.3 years ago • anjanapaleri4

Here is what I've figured out so far: **What data is required to look at allele-specific binding and allele-specific expression?** ChIP-seq is used to look at protein binding sites, so allele-specific...binding type of analyses are done with ChIP-seq data. RNA-seq is used to study gene expression, so allele-specific expression type of analyses are done with RNA-seq data. **How to study allele …

allele-specific-binding allele-specific-expression

updated 2.0 years ago • jgbradley1

In my vcf file, the sum of total allelic depth (AD) is about half of the raw read depth (DP) for all SNPs. Is it common? If not, any thoughts on what might be the reason...bcftools call -mv -Ov ``` The issue remains even if I generate vcf directly from mpileup and sum allelic depth of all alleles not only reference and alternative. Thanks a lot in advance

vcf SNP read-depth Allelic-depth

updated 10 months ago • MH85

There are a number of biostars posts on how to calculate coverage and read depth, and what they mean. I'm still confused. This is how I currently understand things: ## Depth (or Read Depth) at a BP coordinate...The height of the bar over that position in a genome browser. ## Coverage The sum of all the depths across a particular coordinate range such as a gene or a peak. ## Total Read Depth T…

coverage depth read depth

updated 7.0 years ago • ariel.balter

Hello, I am having some difficulties visualizing my depth graph on the IGB software. Is there a way where I can visualize the entire chromosome while keeping the relative size...of the depth graph on the chromosome. Most of the time the max that I can see is one portion of the depth graph, is there a way where I can

IGB

updated 5.2 years ago • jpere716

new to this type of analysis. The NGS sequencing DNA samples I have are with different sequencing depths... Is there any way to equalise all sequencing depths at the level of .bam or .bed files to a particular number of reads, e.g

next-gen sequencing gene

updated 7.2 years ago • sliproach

Can `samtools depth` be used for finding out sequence depths for individual `sorted bam` files? I am not trying to get one value for all the files...altogether. samtools depth ls sorted.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}' > log.txt I want output `(log.txt)` as: File name Average 1sorted.bam -- 2sorted.bam

alignment

updated 4.8 years ago • evelyn

My boss said he wanted to get the read depth graph for each CNV we found. The only data I have is a file with the number of reads aligned to each position (let's say from...we have a CNV deletion identified from position 100 to 150 .. How am I suppose to output the read depth for that CNV

genome sequencing read depth-of-coverage

updated 11.7 years ago • madkitty

Hello. I try to find positions that have higher depth significantly than their surroundings. Is there a good way to do this? Currently I have depth per position data from `samtools...depth

depth python samtools

updated 7 months ago • hyperdx1

Hello, If I have a sample sequenced in two different depths: 15-20M and 80-100M 1) How much difference will there be in the expression(raw count), of a certain coding gene coming from...these two different libraries. 2) Is sequencing depth directly proportional to the read counts? If Yes, then how can we compare genes/features across samples having different...sequencing depth

gene ngs transcriptomics sequencing

updated 3.0 years ago • glady

HG03297.mapped.ILLUMINA.bwa.ESN.low_coverage.20130415.bam.bai I want to compute the depth of coverage for each of bam.bai files. I used samtools depth command /data/programs/samtools-1.3.1/samtools depth NA21142.mapped.ILLUMINA.bwa.GIH.low_coverage.20130415.bam.bai...fail to open file > 'NA21142.mapped.ILLUMINA.bwa.GIH.low_coverage.20130415.bam.bai' > samtools depth: Could n…

depth of coverage samtools

updated 6.0 years ago • Ana

colums in my dataset. But I am trying to understand in particular the difference between reference allele and alternate allele columns. What does it actually explain. It would be really helpful if you make me understand

allele

updated 7.4 years ago • ash

frq format). These files contain the minor (A1) and major (A2) alleles for every SNP. As I understand, minor and major alleles correspond to alternate and reference alleles, respectively...is this correct?). Moreover, I understand that USUALLY reference alleles are the same as ancestral alleles. So, for my SNP list, in order to get their ancestral alleles, I downloaded the file "SNPAncestralAlle…

SNP derived-allele ancestral-allele

updated 21 months ago • Mr Locuace

5,180 results • Page 2 of 104

Recent Votes

Comment: High Malat-1 expression in single cell data

Comment: Gene Specific coverage from WGS data

Answer: ATAC-Seq and RPKM

Answer: MSA and distance matrix in R

Comment: MSA and distance matrix in R

Comment: Which hg38 file?

Answer: Which hg38 file?

Recent Locations • All