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Old 09-05-2014, 09:15 PM   #1
ksw9
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Default Create .bed file from Genbank file

Hi,
I am trying to generate a .bed file of coordinates for a list of genes of interest so that I can extract reads from those regions from .bam files I have generated. Is there a tool for extracting coordinates and generating a .bed file from an annotated Genbank file?

Thank you,
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Old 09-06-2014, 06:04 PM   #2
GenoMax
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A google search found this: https://gist.github.com/brantfaircloth/893580
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Old 09-07-2014, 01:20 PM   #3
ksw9
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Great, thank you!
A related question: Is there a tool to generate .fasta consensus sequences from specific regions of interest? For example, I have a .bam file of all sample reads from which I extract reads of interest with bedtools intersect to create another .bam file. Then, I can use bedtools bamtofastq to generate a .fastq file of the regions of interest, but to then generate a .fasta consensus sequence, I do not want a .fasta covering the entire reference genome, but only the region indicated by the .bed file. Is there a tool for this?
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Old 09-07-2014, 03:33 PM   #4
GenoMax
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Quote:
Originally Posted by ksw9 View Post
Great, thank you!
A related question: Is there a tool to generate .fasta consensus sequences from specific regions of interest? For example, I have a .bam file of all sample reads from which I extract reads of interest with bedtools intersect to create another .bam file. Then, I can use bedtools bamtofastq to generate a .fastq file of the regions of interest, but to then generate a .fasta consensus sequence, I do not want a .fasta covering the entire reference genome, but only the region indicated by the .bed file. Is there a tool for this?
Try this to generate a consensus sequence from your genes of interest:

Quote:
samtools mpileup -uf ref.fa -l your_bed_file aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
Then use seqtk to convert from fastq to fasta.
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Old 09-07-2014, 03:52 PM   #5
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Thanks, just what I was looking for!
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