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16,071 results • Page 1 of 322

Hello, I'm currently following the BBMAP pre-processing guide prior to performing a genome assembly and it mentions normalisation and subsampling for assemblies with high or uneven coverage. Having done a bit of...reading about calculating coverage I was wondering which is best way to go about it? 1) Map reads to a reference genome (reference genome appears to be very...similar, 98% of my reads…

Assembly genome bbtools

updated 7.0 years ago • GLR

I have the read file and assembled contigs (both in .fasta format). I need to calculate the coverage for each single contigs across the read file. I tried...the error **"Splice sequence indexing failed with err =1"**. Kindly help me how to proceed with the coverage calculation of each contig

alignment

updated 4.8 years ago • singh.jyotika

genome and I sequence it into short-reads. Then, I will fed the reads to velvet to create a de novo assembly. Let's say I have two or more contigs assembled (but not the entire genome). velvet also reports k-mer coverage for each...of the contig. For example, if AGCGGCC is my reference genome, my two assembled contigs are AG (the first two bases) and CC (the last three bases). I'm also given k-…

metagenomics velvet

updated 22 months ago • SmallChess

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...before I am having trouble 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

RNA-Seq Assembly next-gen rna-seq

updated 6.1 years ago • babji2318

We have recently sequenced a metavirome using illumina miseq platform (2x300). All the reads were assembled using Spades genome assembler available on illumina basespace using default settings. The output contigs had...In this example what does `LENGTH_43376_COV_6.27809` mean From what I understood cov indicates kmer coverage can this information be used to calculate the actual contig coverage? …

Assembly next-gen-sequencing alignment

updated 2.2 years ago • scarabbeetle

Hi all, I did de novo transcriptome assembly using paired-end reads from Illumina Hiseq 2000 for a non-model organism. I mapped back reads to transcriptome assembly...If I'm not wrong, the average of mapping coverage shows the read number (in average) that mapped to each reconstructed transcript (contig). Could you please let me know...if this number is important and why? and how I can calculate…

read mapping covergae transcriptome

updated 8.0 years ago • seta

this has been asked a lot, but I havent found a tool that fits my simple needs. I would like to calculate coverage % for an alignment file (sam ot bam) against a reference fasta genome. (NB there may be mutiple aligned sequences...in the sam/bam file). bedtools can calculate coverage - but splits this up and I cant work out how to get a single % value for coverage - other than writing a script

coverage

updated 3.4 years ago • daewowo

Hi everyone, I have bed file, bam file of human exome data and i wish to calculate the coverage per gene. Are there any suggestions on how i should calculate the coverage per gene

coverage gene

updated 18 months ago • anii

Is there a way to calculate 5x, 10x, 20x, 30x coverage from a BAM file ? EDIT: I have a BAM file and I want to calculate the percentage of region of interest...with 5x, 10x, 20x coverage. I used Samtools and it gives me a list of coverage values. How is the % region of interest with 10x calculated from these

coverage bam

updated 11.2 years ago • meredith19

illumina and ONT reads of yeast. I would like to know the tool to combine or hybridize and after calculation how to calculate coverage of a specific gene of interest inserted in genomic DNA

gene coverage

updated 16 months ago • ameya4microbiology

I want to calculate the % coverage of my assembly based on reference mapping. Should I use `samtools coverage` or `samtools depth

samtools

updated 2.5 years ago • melissachua90

The information I have is that they're illumina reads with average length 250bp. Now i want to check coverage of all the genome. I did like this: coverage = (read count * read length ) / total genome size. where read count =(wc-l xyz.fastq...length =250 total genome 5.2million bp Can any one please suggest me i am doing write way or my calculation wrong

fastq coverage

updated 10.8 years ago • HG

Dear Friends, I am a beginner in the field of De novo Genome Assembly. I tried to understand coverage cut off and expected coverage parameters in Velvet assembler. But i could not understand...Could anybody explain me what is coverage cutoff and expected coverage in denovo assembly with an example? Thanks in advance

Assembly

updated 8.1 years ago • saranpons3

Hi,everyone , There I want to calculate the RNAseq reads coverage the numbers of genes and sequences from reference genome and I have bam files ,did anyone...knows how to calculate it ? Thanks Alex

RNA-Seq

updated 8.0 years ago • Alex

can someone explain How can I calculate Coverage Uniformity from bam file

ngs bam

updated 2.6 years ago • hafiz.talhamalik

Hi, How do you calculate the coverage of target genes with Haloplex data? I am trying to use GATK but it gives 0 for TP53. However, when I check...the coverage in IGV the gene is well covered... any suggestion? Thanks Sara

next-gen

updated 6.2 years ago • jonessara770

Hi, My output from the assembler SOAPdenovo2 is formatted like this > scaffold148 17.4 > scaffold149 37.1 What is that second number ? Is it the...coverage ? If yes I don't understand what it means in an assembly. I mean the coverage is normally the number of time that a base

Assembly

updated 8.3 years ago • Picasa

I have a question regarding coverage levels of different scaffolds in an assembly to better my understanding of genome assemblies. Say my species of...I have a question regarding coverage levels of different scaffolds in an assembly to better my understanding of genome assemblies. Say my species of interest is the one shown in the orange points in the below example blobplot (produced using [Blobt…

coverage Assembly blobtools

updated 5.2 years ago • yp19

How can I calculate aligned sequence length coverage from the results of protein domains obtained through pfam_scan.pl program...hmm start and end (I don't know) hmm length bit score E-value significance I am trying to calculate the aligned sequence length coverage for each protein and filter the results. Could anyone please suggest me how...can I calculate the same

protein domain pfamscan alignment coverage

updated 4.4 years ago • aiswaryabioinfo

I have Nanopore long read data from several patients. I would like to calculate coverage of the long read data but I couldn't find any tool that does this. I did some calculations myself (SUM (samtools...depth)/total bases) but I'm not sure if this is accurate. Any suggestion of tools or approaches to calculate the coverage for long read data would be appreciated

sequencing coverage

updated 21 months ago • Arton

Hello out there. I was wondering if there is a simple way using R to calculate the coverage of a protein when you have a list of peptides from it and its initial sequence. For example let's say that...AKIKAYNLTVEGVEGFVRYSRVTK", "DRRRRMEALLLSLYYPNDRKLL" , "SEVDVNKMCCWVSKFK") Can we somehow to calculate the coverage ? Thank you

R protein coverage uniprot

updated 7.2 years ago • arronar

Hi All, I have to calculate the coverage for human WGS of illumina sequenced read. After reading the technique note of illumina I have some...doubts in WGS coverage calculation of human sequence. ( https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes...for WGS coverage calculation? if so what is the difference strategy used by illumina platform for calculating c…

next-gen sequencing WGS human illumina

updated 5.4 years ago • Nitha

How to calculate coverage in targeted sequencing using Lander/Waterman equation

SNP Targeted Sequencing NGS Coverage

updated 4.9 years ago • Abdul Rafay Khan

I'm trying to convert the kmer coverage reported in the headers of my contigs into standard coverage. Velvet's manual says the relation between kmer coverage...Ck` and standard coverage `C` is `Ck = C * (L - K + 1) / L` where `L` is the read length and `k` is the chosen kmer length. However, I tried using this formula to calculate...C` given `Ck` for each contig, then calculated the median `C`, …

coverage velvet assembly contigs

updated 2.2 years ago • novice

I have a bunch of viruses I've assembled from metagenomic data and I have the host genome as well. I want to see what proportion of each virus aligns to the...host genome. I ran minimap2 with the host genome as the reference and can calculate the percent of the genome covered using samtools coverage but how can I do this with the reverse? Would it make sense

samtools

updated 9 months ago • O.rka

I have the raw R1 and R2 files of a bacterial genome sequence that have been assembled into contigs using spades. How can I calculate the genome coverage / depth? Thanks

sequencing genome coverage

updated 2.8 years ago • dnaproteinstudy

Having been really pleased with results from the Ray assembler I was a little disappointed to see that there are no coverage statistics in the fasta headers (as there would be in...Velvet). What would be the best way to assess the coverage of each contig assembled? and for bonus points; what would be the easiest way to incorporate the coverage into the...fasta headers? currently looking into m…

Ray metagenomic coverage Assembly QC

updated 9.7 years ago • nfellaby

In order to calculate coverage per bait is the calculation: bait reads / (bait length * 100)? That seems a bit off when I put real #'s to it (158 / (153

exome-sequencing coverage

updated 22 months ago • bioguy24

My metagenomic assembly has low coverage. What upstream steps can I adjust to increase coverage? At what possible cost? Low coverage of metagenomic...My metagenomic assembly has low coverage. What upstream steps can I adjust to increase coverage? At what possible cost? Low coverage of metagenomic assemblies must be a common problem, but I've been unable to find a "quick start guide" i.e. an outli…

metagenomic assembly coverage trimming megahit

updated 6.6 years ago • willnotburn

I have multiple samples (interleaved reads), which were co-assembled into one `final.contigs.fa` assembly. The downstream goal is analysis of gene distribution among the samples, multivariate...did that and got `sam` files, which I converted to sorted `bam` files. Now, I am trying to determine coverage. Questions: **Q1:** *Assembly coverage*. My friend asks: what's your coverage? He means that a…

metagenomics coverage bowtie2 samtools mpileup

updated 6.5 years ago • willnotburn

Hello everyone, Do you know of any tool that allows you to calculate the heterozygosity of an assembly? The genome I have is from a diploid plant

plant assembly Genome genome heterozygosity

updated 8 months ago • sansan_96

I am trying to assembly a chloroplast, which closest reference is 150K long. I have 4.5M pairs (2x100nt). This gives me a coverage of 6000X! And...my assemblies are horrible (long -2 million bases- compared to reference genome of 150K, and remapping reads vs. contigs only 30...or randomly sampling X number of reads? I took a subset of my data for having 100X and I assembled it with Velvet. When …

assembly chloroplast plants coverage

updated 3.1 years ago • int11ap1

Hello Everyone, So I have a Gene Panel with Gene name, I want to calculate gene coverage in a bed file. How can I attain that? I don't have any bam file for that. I want to check coverage of all genes

bed coverage gene

updated 19 months ago • Nikhil

project (Sequel) and after a first run on a single cell, it looks like I will have an overall coverage of 8X (if I continue the run). My knowledge in genome assembly is very small but I am curious to know what folks think: Would...it be OK to do de novo assembly with 8X coverage and good quality fragments of ~ 10kb? I know it is of course possible but I am just wondering if it is

Assembly coverage

updated 6.6 years ago • AP

Hi, I have a list of exons (in BED format) and I wish to find the coverage per exon from a BAM file. I was looking at [Bedtools][1] coverageBED but I don't think that gives me the per exon coverage...Are there any suggestions on how I should go about calculating the coverage of each exon? Also, eventually, I have to also calculate per gene coverage. How do I go about calculating the per gene..…

coverage gene exon

updated 2.1 years ago • thecuriousbiologist

Hi All, I am currently trying to calculate the coverage of polar bear scaffolds in the attempt to compare between male and female coverage. I have used `samtools...but I am unable to select an option which allows me to to choose only called bases in the depth calculation. So my question is whether there is any options which allows you to only choose called bases when calculating...read depth/co…

genome Coverage

updated 7.3 years ago • ThomasL70

Hi guys, I am working with 454 reads with 1x coverage. In order to find centromeric repetition, I was thinking about assembling reads and then trying to recognize repetitive...regions. However, I am not sure how much sense it makes to assembly reads with such coverage. Any help will be appreciated. Thanks. EDIT: Thank you very much for the answers. I decided to...reformulate problem. I have 45…

assembly clustering

updated 12.7 years ago • Biomonika (Noolean)

Dear Biostars, I am trying to remove the transcripts that have less than 0.1 average base-level read coverage. But I am quiet confused with calculation part. Any comments or answers would be appreciated. What if I calculate coverage

rna-seq coverage

updated 11.0 years ago • biorepine

Hi, I have assembled the 3-cells reads data of `PacBio HiFi`. Question is how can I find the coverage of my assembled contigs? I shall be grateful

PacBio assembly coverage

updated 15 months ago • rj.rezwan

Hi all. I'm in the process of uploading a draft bacterial genome assembly to NCBi. NCBI asks that you give a coverage estimate based on #bps sequenced/ expected genome size x % of bps placed in...final assembly. I have calculated this using the kmergenie estimate for expected genome size as this is a de novo project, the numbers...1511690223) = 3086720925 (i.e total bps sequenced) kmergenie geno…

kmergenie genome size coverage

updated 8.4 years ago • cook284

Hi all Does anyone have an idea how I can calculate the number of mapped reads, unmapped reads, and the gene coverage from local BLAST results. The -outfmt 6 option gives...end of alignment in query, start of alignment in subject, and end of alignment in subject. As genome coverage= number of reads + read length/ length of gene, I wondered whether I can utilize these output values to determine c…

blast metagenomics coverage

updated 4.5 years ago • Happy_flower

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...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, …

depth assembly

updated 6.0 years ago • Jane

Hi all, I have some genes which are expressed in differentially compare to wild type, so i want to calculate perbase coverage from the BAM files. How to calculate that one

RNA-Seq next-gen R

updated 5.1 years ago • barrypraveen

Hi! I would be very happy if someone could give any advice about SAMtools. I have used "pileup" to calculate the coverage of each position of my reference genome by mRNAseq reads. Now I have a list of exons in bed format and

pileup coverage samtools

updated 13.2 years ago • Cdiez

Hi Everyone, I want to calculate the percentage of reads that my assembled contigs cover across the entire metagenome (paired-end). I generated the...Hi Everyone, I want to calculate the percentage of reads that my assembled contigs cover across the entire metagenome (paired-end). I generated the alignment file of mapped reads using BBmap as: ``` bbmap.sh ref=contigs.fasta \ in1=metagenome.R1.f…

coverage metagenomic fasta bbmap alignment

updated 22 months ago • shail.nair05

Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly...Command** bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt **I got output like this:** #ID Avg_fold Length Ref_GC Covered_percent Cove…

coverage average assembly

updated 2.2 years ago • davidmaimoun

on from a public database. But I do have exon counts for these. I'm wondering if I can use these to calculate coverage where I can take the average of the RPKM X Length of transcript, which would reflect the total read coverage

rna-seq

updated 14 months ago • unawaz

Any recommendation for packages to calculate alignment coverage from bam/sam files? 1. I need whole genome-wide calculation instead of certain genomic regions

coverage

updated 12.8 years ago • Bioscientist

of a bioinformatics newbie and need some help. I was wondering if it is possible to determine the coverage of a single gene from whole-genome sequencing data? I have the target gene sequence, the R1/R2 reads, the whole-genome...assembly, and a reference genome assembly. I expect this target gene to be present on a plasmid and therefore potentially present...in multiple copies. As a rough esti…

SNP Assembly genome alignment sequencing

updated 5.2 years ago • sarah.goldstein

Hello, I am trying to do a de-novo assembly of a turtle genome of about 2.15 gbases with Nanopore Minion reads. I have read about Canu as a good tool for this purpose...but it seems it yields good a good assembly with reads of at least 20x coverage, and the coverage of my reads is only about 2.5x. Is this value too low for de novo...assembly with Nanopore reads? What would be a good coverage valu…

Assembly assembly sequencing ont

updated 5.7 years ago • marianaer98

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