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Posts by chparada
... 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`. ...
... 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 ...
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