User: maricom

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maricom0
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Posts by maricom

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Comment: C: operon for rRNA genes
... Thank you for your response! Yes I was thinking that way. This is an Illumina-only draft assembly. I found the location for each rRNA genes, but still isn't it possible to recognize the operon for each genes?? ...
written 3 months ago by maricom0
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operon for rRNA genes
... Hi all, I have a draft genome of bacterial gene and try to find out whether it has an operon for respective rRNA genes (5S, 23S, 16S). I found that it has all three rRNA genes using RNAmmer, however, I'm not sure how I can find their operons. If you have any idea, I would really appreciate that. ...
rrna operon written 3 months ago by maricom0
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Comment: C: snpEff for bacteria genome
... Hi, Thank you for your reply. I obtained this genome, so I created db. GTF file is like this. seqname source feature start end score strand frame attribute bacteria1 bacteria1 CDS 101 1507 . + 0 gene id "bacteria1_0001"; bacteria1 bacteria1 CDS 1569 26 ...
written 4 months ago by maricom0
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snpEff for bacteria genome
... Hi all, I'm trying to annotate bacteria genome using SnpEff. Variants were detected using gatk HaplotypeCaller. I'm wondering what kind of options do I have to use for bacteria genome? My current command is like this. java -jar snpEff.jar -c snpEff.config -i vcf -o vcf database input.vcf > ...
snpeff written 4 months ago by maricom0
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Answer: A: gatk HaplotypeCaller options
... Thank you! I'll check which is appropriate for my case. ...
written 4 months ago by maricom0
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gatk HaplotypeCaller options
... Hi, I am counting variants using gatk HaplotypeCaller, however, I am not sure the difference between two options, MappingQualityReadFilter and MappingQualityFilter. I read the documents, but still it's not clear to me. Could anybody give me more detailed explanation for them?? MappingQualityReadFi ...
gatk written 4 months ago by maricom0
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Comment: C: Warning errors in snpEff annotation results
... Hi SMK, Thank you for your advice! I've sent the question to him, too. ...
written 4 months ago by maricom0
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Warning errors in snpEff annotation results
... Hi, I annotated variants in a bacterial genome using snpEff, but when I saw snpEff_summary.html, there were 944 warnings colored in yellow. Varians were detected using gatk HaplotypeCaller. When I saw the warnings, they were almost WARNING_TRANSCRIPT_NO_START_CODON. However, when I checked both re ...
snp written 4 months ago by maricom0

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