User: Mbillah

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Mbillah110
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110
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Chittagong
Last seen:
1 month ago
Joined:
10 months, 2 weeks ago
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Posts by Mbillah

<prev • 65 results • page 2 of 7 • next >
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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 8 months ago by Mbillah110 • updated 3 months ago by Mant0
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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 8 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 8 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 8 months ago by Mbillah110
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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 8 months ago by Mbillah110
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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 8 months ago by Mbillah110 • updated 8 months ago by ATpoint21k
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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 9 months ago by Mbillah110
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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 9 months ago by Mbillah110
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Comment: C: How sickle (adaptive trimming tool) work.
... I also got this article, but i didn't understand exactly, what parameters should we use & how can i select those parameters? I got only two parameters that are length and quality threshold, is there any other parameters? Did you use it before? if yes, then it will be very nice if you share you ...
written 9 months ago by Mbillah110
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How sickle (adaptive trimming tool) work.
... I am trying to understand how "sickle - A windowed adaptive trimming tool for FASTQ files using quality" work. Can any explain with a example if they have worked with this tool before? Which one is best - trimmomatic or sickle? I have paired end, illumina hiseq 2000 reads. Thank you ...
sequence written 9 months ago by Mbillah110 • updated 9 months ago by Pierre Lindenbaum122k

Latest awards to Mbillah

Rising Star 8 months ago, created 50 posts within first three months of joining.
Student 9 months ago, asked a question with at least 3 up-votes. For Implement ensembl gene annotation pipeline for my assembly
Supporter 9 months ago, voted at least 25 times.

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