Biostar

16,071 results • Page 2 of 322

Usually when we assemble PE (100, 150, 250, 300) fastq Illumina data we see that roughly the expected theoretical coverage is close to the actual...coverage over de novo assembled contigs using for instance SPAdes. However I currently have an older dataset PE 76->51 bases...with a theoretical coverage of over 200 fold. However when I inspect the assembly the average coverage is only ~5 fo…

Assembly SPAdes de-novo bacterial-species

updated 2.1 years ago • ALchEmiXt

a BAM file from human whole exome sequencing data. I am looking for a tool (Windows OS) that can calculate the coverage for specific gene output. For instance, I am using VarAFT Tool. I can look at specific gene, let's say PKD2...and the tool can output coverage 1x (100%), coverage 5x (95.2%), coverage 10x (93.5%), coverage 20x (90.1%) and coverage 30x (82.7%). I am trying to look for spec…

Coverage

updated 3.3 years ago • koay

bacterial genome with an average read length of 100bp, sequenced from Illumina platform. I want to assemble this genome. It would be really nice if you would help me with some queries... Will SPADES be a usefull assembler for such...low read length ? How can I select an reference genome for this bacterial genome ? How can I calculate the coverage of the genome ? Thank you

sequencing

updated 7.6 years ago • glady

Hello, I am looking for a calculation of gene coverage from the BAM file or any other file used in whole-exome data analysis. Please tell me if anyone

WES

updated 3.0 years ago • smrutimayipanda

Hello, I have been using qualimap to generate stats of the bam files I got, including coverage. Recently, I am getting crashes because there is not enough memory, even if I use the memory parameter `--java-mem-size...20000M`. Is there another way to calculate the mean coverage of a bam file? I have tried with `bedtools genomecov -bga FILE.bam > FILE.coverage.bed` but I got

bam qualimap coverage

updated 3.5 years ago • marongiu.luigi

of NGS sequencing data and have some questions regarding the methodology for calculating base coverage using .bam files. Initially, I merged the .bam files and utilized the samtools depth command to calculate the coverage...were aligned to the same reference. As an alternative, I calculated the coverage for each sample individually and then computed the average base coverage for each gene. Howe…

samtools ngs coverage

updated 1 day ago • slzr_

Hello, I am using Canu 1.4 on a unix machine. I am trying to assemble a eukaryote genome with a lot of repeats. We have PacBio datas, and a coverage ~35x. We are obtaining quite good results...misjuction among out final contigs. I wanted to know if there is a possibility to require a higher coverage during the trimming and assembly phases. thank you in advance. Celine

Assembly genome

updated 6.9 years ago • celine.petitjean

I have a bam file and I have a bed file with my region of interests. Now I'm interested in the mean coverage for each of these region. That's no problem with picard's CollectHsMetrics and the PER_TARGET_COVERAGE flag. But...now I would like to exclude those reads in coverage calculation that doesn't overlap my target region with a given fraction or at least given bases. I feel that bedtools

bam bedtools coverage

updated 6.8 years ago • finswimmer

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 of calculating the coverage in short read is read_length * #_aligned_reads which gives 88 * 36385382. But, when we say coverage, it's represented as...static length genome is covered 40 times with reads). Any help would be apprec…

rna-seq short-read long-read

updated 6 months ago • shinyjj

Hello, I have some troubles calculating the number of reads that I should expect for a target sequence (for instance a trasposon) integrated into the human genome. That is: how many reads should I expect to map to my target sequence and confirm the presence of the target? Assuming: 1) a pre-calculated coverage of 20, 2) a target region of 1000 bp and 3) a fixed length read of 150 bp and using …

Assembly genome sequencing

updated 6.8 years ago • marongiu.luigi

Hello, I am wondering whether MuSiC uses soft-clipped bases in its coverage and background mutation rate calculations. I have generated somatic variant calls from WES tumor/normal pairs...using MuTect2 with the --dontUseSoftClippedBases option, and I want to be sure that the coverage used for the bmr calculation matches the coverage that was actually used for calling variants. I'm not sure if …

music soft-clipped bases calc-covg

updated 7.1 years ago • kmegq

HI, if i'm sending samples for sequencing at say 30X coverage of a given genome, what is the relation between the 30X,40X coverage metric and the minimum number of reads that i should

next-gen coverage

updated 5.5 years ago • Raygozak

name and to have the same number of reads per fastq file. I want to use these reads to do *de novo* assembly. For chloroplast, I have a total coverage of 5600x. Doing sampling to have a 60x or 90x of coverage, and kmers of 37,47,57...67 or close, I get a highly fragmented assembly. For mitochondria, I have a total coverage of 1400x. Doing sampling to have a 60x of coverage and kmers 47,57,67…

assembly genome next-gen sequence alignment

updated 5.3 years ago • macielrodriguez2

Hi, I'm using SPAdes to assemble bacterial genome sequenced on illumina platforms. I have a few files that I'm struggling to assemble due to the incredibly...large coverage of my raw reads. Anything over 250x seems to cause spurious assemblies, with the final fasta being three times the...shows only target species genes present. I've heard SPAdes can struggle with particularly high coverage fil…

Assembly illumina spades

updated 8.6 years ago • b2060780

I want to calculate coverage for a CRAM file. I want to see how the coverage varies by chromosome in different genomic regions and apply...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 7 months ago • prds

the RNA sequencing of one sample on the one lane of Illumina Hiseq2000. After making transcriptome assembly and mapping read back to the assembly, I found that the average coverage is about 400, and there are about 15000 contigs...with zero coverage. My question is: if can I remove the contigs with zero coverage from the initial assembly before annotation step and

mapping zero coverage transcriptome assembly

updated 8.8 years ago • seta

I am trying to assembled a pooled metagenomic dataset with 762909004 reads. Will using tools such as BBNorm to downsize the coverage in...order to speed up the assembly significantly effect the final assemblies

Assembly

updated 3.9 years ago • robert.murphy

to investigate the read the cover the reference more than 80%. I know that samtools can be used to calculate coverage and depth for the interested regions but what about each read? For example, I have read 1-10 that cover region...A, I want to know their percent coverage for all of each read. Expect output: read 1 70% cover, leftmost position 1 (like sam format column) Is there any tools or

alignment nanopore sequencing

updated 3.5 years ago • sonsunjirachote

Hi, I would greatly appreciate some help with my problem. I have just assembled denovo a genome from Illumina 100bp paired end reads, using SOAPdenovo2 and then GapCloser. My total scaffold...Hi, I would greatly appreciate some help with my problem. I have just assembled denovo a genome from Illumina 100bp paired end reads, using SOAPdenovo2 and then GapCloser. My total scaffold length...33…

coverage denovo genome assembly

updated 11.2 years ago • AW

I want to calculate the total base pair of coverage of Genome re-seq data on IGV Is there anything tools on IGV ? Sorry for my bad English

IGV

updated 4.0 years ago • KIOA

Hi everyone, I wanted to see the effect of coverage on the assembly quality to see at which point there is a diminishing return. I am using paired-end reads only (101x2...with 520 insert size), no mate pairs or long reads. Normally a higher coverage is supposed to increase NGA50, but instead, the contig NGA50 has gone down while the LGA50 has gone up. I have five levels...of coverage: 10X, 15X, …

Assembly next-gen Coverage alignment genome

updated 5.8 years ago • AXR

Hi all I am struggling to find a tool for extracting the read depth information and sequence coverage. I know their information is very important before variant callings. It is necessary tasks. I found some good tools...failed. What I want is align information as below: **For example**: ``` total_coverage(X) : 93.22 coverage 1X : 99.96 coverage 2X : 99.9 coverage 3x: 98.4 ..... coverage 97X : …

next-gen alignment

updated 2.3 years ago • mangfu100

Hello everyone! I'm planning to use proovread to correct some PacBio sequences and use them to assemble a plant genome (around 400 Mbp). I currently have 30x coverage of PacBio data, 88x coverage of HiSeq2000 data and 24x...coverage of MiSeq data (after quality filters and paired-end merging of Illumina sequences). The proovread manual suggests...a coverage around 30-50x. Is there any reason, …

genome Assembly hybrid PacBio Illumina

updated 8.2 years ago • Josué Barrera

Hi all, We are sequencing a fish species using ONT long reads. We have assembled the genome using Flye. The first assembly we did with about 22X coverage, and we got the following metrics: No. contigs...runs, which were not perfect in terms of yield, but gave us better N50 distribution and we did an assembly with 32X coverage. While most metrics stayed the same, the N50 actually decrease…

Minion genome assembly flye sequencing

updated 3.3 years ago • roger.huerlimann

Hi, I'm trying to find tools to calculate uniformity coverage. I tried use bedtools to get the depth metrics but it takes a really long time. I'm wondering if

exome sequencing

updated 7.1 years ago • jackyen

Hi! When performing genome assembly, it usually need high coverage data, such as more than 50X for pacbio, in my opinion, 10X would be enough to correct the...high-error reads and assembly the genome. Considering we can't get the uniform coverage across the genome, thus we increase the total coverage to...were covered by 10 reads to perform correction. Also, as for illumina and sanger data, the …

genome Assembly PacBio Coverage

updated 7.9 years ago • lamz138138

Dear Sir/Madam, I have single end data (Ion Torrent) and de novo assembly performed with MIRA (660 contigs) and SPADES (753 contigs). I just blasted few contigs it showed very less query coverage...17% of 63000 bp) and comparatively less identity (81%). Also performed reference assembly. Only 3% of the total reads aligned to the reference genome. 1. Why query coverage is very less? 2. Why less …

next-gen Assembly blast

updated 23 months ago • chullijoby

we did some genome sequencing of bacteria from a biotech company, They used de-novo assembly for sequencing with Shovill assembly method using Illumina NovaSeq I need to submission those genome data in NCBI...but the problem I am facing with their provided modifier details they mentioned genome coverage of a bacteria eg. 497 Could anyone make me understand what it literally means? I know t…

genomics Illumina Novaseq

updated 12 months ago • microorganism_001

Dear all, I have assembly my reads with MEGAHIT to get final contigs. Then I mapping back my contigs with raw reads to get coverage rate with...in=IA.sam.gz out=IA_mapping.txt hist=IA_histogram.txt I got result like this: Average coverage: 4.25 Percent scaffolds with any coverage: 99.91 Percent of reference bases covered: 98.83 How to interpret the result

assembly metagenomic next-gen

updated 4.5 years ago • nisrinalulu

Hello for WGS, when a given depth of coverage is recomended, for example: 30x for variant calling, where does that quantitiy derive from?: A/ from raw reads (number...through several threads in this forum and in the literature, but I find no consensus on depth of coverage calculation. I am mostly confused about wheather it takes into account the reads before or after alignment. Is there

coverage SNP WGS dnaseq depth

updated 6.2 years ago • serpalma.v

I'm using the equation Num_Reads * Avg_Read_Length / Genome Size To calculate coverage. Here are my questions 1. Should I only consider mapped bases in the Query to calculate the read length? Specifically...would the read length be 60 since 10 were not aligned properly? 2. Given 1. why is it that my calculation of coverage differs from `samtools mpileup`? Wouldn't the average of column…

samtools bamtools coverage

updated 7.5 years ago • QVINTVS_FABIVS_MAXIMVS

Hi all, I would like to have a plot of coverage vs GC content for a assembled transcriptome. Could you please introduce me any tool for it? Thanks

plot transcriptome assembly coverage GC content

updated 9.0 years ago • seta

Hi friends I want to calculate average of read count / coverage for all genes, I mean creating a list which shows number of aligned reads for each

wig bam

updated 8.4 years ago • Whoknows

Hello, I was wondering if anyone knew how to calculate the coverage of a specific genome using output metrics from Oxford Nanopore Technology. For instance, can anyone...calculate coverage information using the total number of pores ran, the N50, and the data in Gb? Information of the expected

oxford nanopore coverage

updated 4.7 years ago • AP

specific transcript isoform. I wanted to perform a Differential Expression analysis using a genome assembly without a gene annotation, as a reference. To do this I have aligned the reads using STAR and then pooled all the alignments...into a single bam file. To assemble the transcripts and annotate the reference I used stringtie. After this I used the gtf output of stringtie as a reference...to…

stringtie differential-expression

updated 13 months ago • Tihana

bam files (in different conditions) and a bed file with specific genes of interest. I would like to calculate the coverage for each bam file over my gene list. What I am doing is, for each condition: bedtools multicov -bams *cond1.bam...bed exon.bed > multicov_condition3_exon The final idea is to identified in which condition the coverage is higher. Is that a good option to analyze …

RNA-Seq exon coverage multicov bedtools

updated 7.4 years ago • Lila M

Hi, I have a query regarding reads assembly I have a bam file I made a consensus sequence but I want to make a consensus sequence with a minimum of 2 coverage per...site instead of full coverage I want to compare substitution changes but only I found full coverage is only in my consensus sequence. I want to extract...in a consensus. I have used the following command to make a consensus can we …

bcftools Samtools

updated 3.1 years ago • Info.shi

Hello, I have to work with a genome assembly which consists of about 32000 scaffolds (obviously, the scaffolds are not annotated) as a reference for SNP calling...However, before proceeding further, I would like to: 1. Read about the process of making a genome assembly. 2. Get basic statistics of my genome assembly. I have been searching to find a good review but I thought to ask if there...fi…

Assembly

updated 2.6 years ago • thjnant

Good afternoon, I'm working with target capture sequencing and I would like to know the coverage of my target genes, which I just have in fasta format. I already have my reads aligned into the genome and in bam format...and I also already did the SNP calling (with freebayes). So my questions are: - How can I calculate the coverage of my target genes in the bam files I have? - Could be a way to …

coverage target capture target capturing BAM VCF

updated 4.5 years ago • gubrins

for which macs gives multiple, different fold changes, p-values, and q-values. However, when I calculate their coverage using `bedtools multicov` I get the exact same coverage (as I would expect). What calculation is `macs2

macs2 ChIP-Seq

updated 7.8 years ago • ariel.balter

I would like to 1) extract reads that aligned concordantly exactly 1 time and 2) then calculate the coverage for each: the number of nucleotides in aligned concordantly reads/the number of nucleotides in the...reference (and then filter by coverage). Please tell me how to do this? Thank you very much in advance! Best regards, Poecile

hisat2 sam mapping coverage samtools

updated 2.7 years ago • poecile.pal

I have assembled bacterial genomes using SPADES. Now I am going to submit them to Genbank, but I need to know the coverage of each assembly...Should I provide the raw read coverage or the filtered final coverage? If the second possibility is true, how do I access these values from the SPADES log

SPADES genome coverage

updated 3.1 years ago • fhsantanna

I am assembling a genome using Canu 2.2 with the following commands on a slurm cluster: ``` canu useGrid=false \ -p tf -d tf-pacbio \ genomeSize...I am assembling a genome using Canu 2.2 with the following commands on a slurm cluster: ``` canu useGrid=false \ -p tf -d tf-pacbio \ genomeSize=164.4m \ -corrected \ corMhapSensitivity=normal \ -pacbio SRR23272336_1_corrected.fastq ``` The i…

Pacbio assembly Canu Genome

updated 14 months ago • Yao

gridss) as Structural variants. But for using Clove I need to specify two values 1. Mean coverage value. 2. Variance of coverage value. So is there a method or tool where I can calculate these values from my bam File

sequence coverage

updated 16 months ago • ash

Hi, I'm interested in gene copy number and normally I calculate read coverage after aligning the reads to a reference, assembling the genome (using said reference), and compare...coverage across gene A, versus coverage across gene B. But I wondered if the process can be speeded up: Find the number of reads...containing parts of gene Ain the contigs, without having to align to a reference an…

CNV software

updated 2.5 years ago • keypuncher

Does the mosdepth exclude the soft clipped bases present in the aligned reads to calculate the coverage? Default it exclude the mark duplicate and secondary alignment reads (`-F 1796`) and avoid double counting

samtools depth wgs mosdepth

updated 16 months ago • kani

I just assembled a plasmid using Illumina 2x250 PE. I am pretty confident that the assembly is fine. I check by mapping the raw data...to the assembly. In general I have a very high coverage (sometimes more than 1000x). Also I have very few unmapped pairs. But I have some...regions where the coverage drops to 10-20 fold coverage. This looks concerning, but I still think my assembly is fine beca…

illumina coverage paired end

updated 9.1 years ago • mschmid

Hi all. I download illumina fastq file via ncbi sratoolkit . Now I calculate the coverage by calculating average depth with samtools But the answer is like 16.12 or 18.07, so I guess the coverage...may be x20 Is there any information I can directly get the coverage information with the access number(like SRR065390), Thanks for your help

genome next-gen sequencing alignment coverage

updated 7.3 years ago • jianzheng934963534

1. PanDepth is a high-performance tool for calculating coverage in sequencing data, outperforming other tools in speed for both BAM and CRAM-format alignment files, regardless...choice for large-scale genomic data analysis. 4. The statistical results of PanDepth on depth and coverage are completely consistent with samtools. You can get the PanDepth code and manual on github [here][1] ![enter i…

bam paf depth cram coverage

updated 9 months ago • Huiyang

Hi. I'm trying to calculate my sequenced bacterial genome's genome coverage (for NCBI submission) but I'm not sure if I got the right answer. According...to biostars.org/p/208339 , the formula is C = R X L / G where C is the coverage, R is the total number of reads, L is read length, and G is the genome size. The total reads (R) that I got for my genome is around...from FastQC when I submitt…

NCBI Genome Sequencing

updated 18 months ago • apcreyes29

16,071 results • Page 2 of 322

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