Question: poly ploid consensus seq generation
0
gravatar for fatimarasool135
10 months ago by
fatimarasool13540 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 • 246 views
ADD COMMENTlink written 10 months ago by fatimarasool13540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1939 users visited in the last hour