User: Mbillah

gravatar for Mbillah
Mbillah100
Reputation:
100
Status:
Trusted
Location:
Chittagong
Last seen:
1 day, 22 hours ago
Joined:
3 months, 1 week ago
Email:
m**********@gmail.com

Posts by Mbillah

<prev • 57 results • page 1 of 6 • next >
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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 9 days ago by Mbillah100
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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 15 days ago by Mbillah100 • updated 8 days ago by lieven.sterck3.4k
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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 5 weeks ago by Mbillah100
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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 6 weeks ago by Mbillah100
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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 6 weeks ago by Mbillah100
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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 6 weeks ago by Mbillah100
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Comment: C: Variants calling by bcftools
... I think sometimes mitochondrial genome increase the read depth, so that I deleted it. Thank you ...
written 6 weeks ago by Mbillah100
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Variants calling by bcftools
... By this following command I want to detect SNPs and indel. Can any one check my step please? Alignment with mitochondria: bwa mem -t 8 \ -R '@RG\tID:1\tLB:1\tPL:ILLUMINA\tSM:1' \ mt_reference.fasta data1.fq.gz data2.fq.gz > aln-mt.sam Unmapped read: ...
indel alignment snp written 6 weeks ago by Mbillah100 • updated 6 weeks ago by ATpoint12k
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Comment: C: mapped reads and unmapped reads not equal total number of reads
... Align: `bwa mem -t 8 -R '@RG\tID:1\tLB:1\tPL:ILLUMINA\tSM:1' mt.fasta read1.fq read2.fq >aln-mt.sam` Unmapped read: `samtools view -@ 12 -b -S -f 12 aln-mt.sam > unmapped.bam` Mapped read: `samtools view -@ 12 -b -S -F 12 aln-mt.sam > mapped.bam` ...
written 7 weeks ago by Mbillah100
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mapped reads and unmapped reads not equal total number of reads
... To remove mitochondria , align with mitochondria reference and reads. After that I collect mapped reads and unmapped reads. But mapped reads + unmapped != total number of reads, Why? ...
alignment written 7 weeks ago by Mbillah100

Latest awards to Mbillah

Rising Star 6 weeks ago, created 50 posts within first three months of joining.
Student 9 weeks ago, asked a question with at least 3 up-votes. For Implement ensembl gene annotation pipeline for my assembly
Supporter 9 weeks ago, voted at least 25 times.

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