User: Mbillah

gravatar for Mbillah
Mbillah110
Reputation:
110
Status:
Trusted
Location:
Chittagong
Last seen:
2 weeks, 4 days ago
Joined:
5 months, 1 week ago
Email:
m**********@gmail.com

Posts by Mbillah

<prev • 61 results • page 1 of 7 • next >
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MD5 for EBI VCF file submission
... Recently I am trying to submit vcf file to EBI(European Bioinformatics Institute) database. In EVA_Submission_template they want md5 value and md5sum value of fasta file. How can I generate md5 value? Thanks in advance ...
md5 snp written 22 days ago by Mbillah110 • updated 22 days ago by b.nota6.2k
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Run abacas for multiple scaffold (20k +)
... I have a scaffold.fa file which contains more than 20K scaffolds. Now I want to run abacas among them. Abacas wants a single query sequence. But I have more than 20,000 sequences scaffolds. So this is not possible to do one by one. How can I do this? ...
assembly written 27 days ago by Mbillah110
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dbsnp for capra hircus
... Can anyone suggest me a dbsnp for Capra hircus(goat)? Recently I find out variants of a goat breed now I want to add rs id to this SNPs so I need dbsnp. ...
indels snp variants written 4 weeks ago by Mbillah110
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Duplicate variants in same position: bcftools
... I create a vcf file by bcftools mpileup command. But I got the huge number of duplicate variants. Duplicate means it shows different variants in the same position. How can I handle this situation? Example: chr1 3993567 T A chr1 3993567 tc t ...
vcf bcftools written 5 weeks ago by Mbillah110 • updated 5 weeks ago by zx87546.7k
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abacas assembly contig to chromosome
... I using abacas to perform contig to chromosome assembly. Abacas spread is too much slow. My contig size is 2.2 GB and all contig size is greater than 200 bp. Abacas do not support threads and multiple cores and it takes 6-7 days to perform single chromosome assembly. Is there any way to spread up th ...
assembly written 10 weeks ago by Mbillah110
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blastx to compute complete, partial or missing genes
... I have a protein sequence and a chromosome. Now I want to find out how many complete, partial or missing genes in my chromosome by the blast. So that I used blastx program, Now how can I determine complete, partial or missing genes from the blast output. ...
gene blastx blast written 11 weeks ago by Mbillah110 • updated 10 weeks ago by lieven.sterck4.1k
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Merge CNVnator and Lumpy to find out copy number variants
... My aim is to find out copy number variants. I knew that CNVnator is enough to find out CNV. Recently I read a post from GitHub. Where they merge CNVnator and lumpy pipeline. Post link: https://gist.github.com/ryanlayer/38b58ef08a5ef7dbe326 Can anyone explain please? Thank you ...
svs cnvs written 3 months ago by Mbillah110
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Comment: C: Genome Size Estimation
... `https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/` `n = [( L - k ) + 1 ] * C` `n = [(150-51)+1]* 123742407` = 12374240700 `N = n / C = 12374240700 / 123742407 = 100` Here, sequence length 150, k-mer length 51 and total read 123742407 What is my wrong ? ...
written 3 months ago by Mbillah110
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Comment: C: Genome Size Estimation
... I have found other formula: Estimate genome size `N = M * L / (L - K + 1) ` `N is Depth of Read Coverage ` `M is mean k-mer coverage` `L is read length ` `K is k-mer size ` `G = T / N ` `G is the genome size ` `T is the total number of bases ` In my side here, L=150, k=51 am I right? How ...
written 3 months ago by Mbillah110
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Genome Size Estimation
... Recently I read a paper where they estimate their genome size by this formula: `G = k-mer number/k-mer depth` `Where, k-mer num=52 413 427 492, K-mer depth = 17` Now, I want to estimate my genome size, where I have 123742407 paired reads and sequence length is 150 bp. if I select kmer as 51. What w ...
genome written 3 months ago by Mbillah110

Latest awards to Mbillah

Rising Star 3 months ago, created 50 posts within first three months of joining.
Student 4 months ago, asked a question with at least 3 up-votes. For Implement ensembl gene annotation pipeline for my assembly
Supporter 4 months ago, voted at least 25 times.

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