User: chparada

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chparada10
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Posts by chparada

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ERROR running STRUCTURE in command line
... Hi! I am trying to run STRUCTURE from the command line using [Structure-threader][1]. This is the error that I am getting: ---------------------------------------------------- STRUCTURE by Pritchard, Stephens and Donnelly (2000) and Falush, Stephens and Pritchard (2003) ...
software error hpc popgen structure written 6 months ago by chparada10
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Comment: A: Generating consensus sequence from bam file
... Thank you for your answers. I meant obtaining the most frequent nucleotide in each position. From the mapped reads, I want to been able to obtain a consensus sequence in single fasta file. I am going to try `bcftools mpileup`. ...
written 14 months ago by chparada10
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Generating consensus sequence from bam file
... Hi, I am trying to generate consensus sequence from a bam file obtained after mapping SRA reads to a reference genome. I used the following commands: bwa mem ref.fasta SRR_1.fastq SRR_2.fastq > bwa.sam samtools view -b -F 4 bwa.sam > bwa_aligned.bam samtools index bwa_aligned.b ...
genome fasta samtools bwa written 14 months ago by chparada10 • updated 4 months ago by vsingh20

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Popular Question 14 months ago, created a question with more than 1,000 views. For Generating consensus sequence from bam file

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