Question: poly ploid consensus seq generation
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gravatar for fatimarasool135
10 weeks ago by
fatimarasool1350 wrote:

Hi everyone, I want to generate polyploid consensus sequence for wheat from BAM file for purposes of retrieving the specific sequence of one transcript/ gene.i want to fetch the sequence of transcript/gene abc from rna seq of wheat.what should i do for that?

my command line is: samtools mpileup -uf reference_cdna.fa Batis_Aligned.bam | bcftools call -c --ploidy | vcfutils.pl vcf2fq > Batis_cnpolyploids.fastq but i found this error

call: option '--ploidy' requires an argument

snp rna-seq assembly genome • 132 views
ADD COMMENTlink written 10 weeks ago by fatimarasool1350
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