User: Lakshman Teja

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Posts by Lakshman Teja

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Bowtie2 error with single end mapping
... Hello, You Just try the below command **bowtie2 -x bowtie_index -U read.fastq -S alignment.sam --no-unal** ...
written 3 months ago by Lakshman Teja0
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Answer: A: SNP calling through bcftools
... Hello, You can use below commands ## Generating variation BCF(binary) file for variation ~/Programs/samtools-0.1.17/samtools mpileup -ugf mtb_h37rv.fna aln_sorted.bam | ~/Programs/samtools-0.1.17/bcftools/bcftools view -bvcg - > var.raw.bcf ## Converty BCF(binary) variation file to VCF(text) va ...
written 3 months ago by Lakshman Teja0
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Answer: A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
... you can use Quast (QUality ASsesment Tool) , evaluates genome assemblies by computing various metrics, including: 1. N50: length for which the collection of all contigs of that length or longer covers at least 50% of assembly length 2. L50: The minimum number X such that X longest contigs cover a ...
written 3 months ago by Lakshman Teja0
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Comment: C: GD::Graph install 'make' failure in Cygwin
... Try **sudo apt-get install libgd-graph-perl** ...
written 3 months ago by Lakshman Teja0
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Answer: A: Bowtie2 parameters for best alignment
... First, you have to build a database, similar to how blast works. This is done by writing: **user@ubuntu$ bowtie2-build -f file.fasta dbname** This will build a database for the "file.fasta" file with the prefix "dbname". To then run the bowtie2 analysis, you need to declare the database, forward ...
written 3 months ago by Lakshman Teja0
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Comment: C: Build Bowtie2 2.3.3.1 with make on linux 64 bit
... Hello, you first install the Threading Building Blocks library, but if unable to do so please specify make NO_TBB=1. TBB comes installed by default on many popular Linux distros. Please note, packages built without TBB will have -legacy appended to the name. **Install TBB library:** sudo apt-ge ...
written 3 months ago by Lakshman Teja0

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