Question: poly ploid consensus seq generation
0
gravatar for fatimarasool135
6 months ago by
fatimarasool13520 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 • 186 views
ADD COMMENTlink written 6 months ago by fatimarasool13520
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: 931 users visited in the last hour