identify the coordinate for coding and non_coding region.
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17 days ago
G.S ▴ 10

Hi,

I would like to calculate the beginning and end positions for the coding and non coding regions in my genome sequence. is there any tool or script to do this ? my consensus sequence differ than the NCBI sequence. It has N stretch at the beginning.

Any help would be much appreciated. Thanks in advance

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coding non_coding • 220 views
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Why do you have those N's at the beginning of the sequence? If the remainder of the sequence matches 100% then the initial N's may be wrong in your assembly.

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mmmm I am not sure. This is how I generate my consnsus sequence

 # Get consensus fastq file
samtools mpileup -uf  KT992094.1.fasta  seq-89_markup.bam | bcftools call -c | vcfutils.pl vcf2fq > seq-89_markup_sorted.fastq

# Convert .fastq to .fasta 
seqtk seq  seq-89_markup_sorted.fastq > seq-89.fasta
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