User: sambioinfo2018

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Posts by sambioinfo2018

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Comment: A: BLASTp in python (solved)
... How did you solve the path issue ...
written 5 weeks ago by sambioinfo20180
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Comment: C: Polyploidy found, and not supported by vcftools
... Thank you Fin for your suggestion. ...
written 11 weeks ago by sambioinfo20180
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Comment: C: Polyploidy found, and not supported by vcftools
... Hi Fins, Thank you for your reply. Yes, the genome i am working is hexaploid. I have tried calling SNPs for the genome using freebayes software. I would like to filter the SNPs from the vcf file based on dept and quality of SNPs. Thank you! ...
written 11 weeks ago by sambioinfo20180
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Polyploidy found, and not supported by vcftools
... Dear All, I am getting the following error while running vcftools for polyploidy genome. Error: Polyploidy found, and not supported by vcftools: 1A:3380 I ran the following script to see the polyploidy: zgrep -v "^#" sample.vcf.gz | cut -f 10- | cut -d ':' -f 1 | sort | uniq And i get: ...
tool snp written 11 weeks ago by sambioinfo20180 • updated 11 weeks ago by genomax65k
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how do i set a 2% mismatch parameter in bowtie
... Dear All, How can I set a 2% maximum mismatch in bowtie2 for aligning the reads to the reference genome? Thanks! ...
alignment written 3 months ago by sambioinfo20180 • updated 3 months ago by genomax65k
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Comment: C: Multimapping reads intervention in SNP calling
... Thanks ATpoint for your detailed reply. I indeed also provided mapping quality and base quality using samtools mpileup. My objective is to call SNPs so in that case bowtie should be sufficient as you mentioned. One more clarification. I have the sequence data from 5 different lane for the same sampl ...
written 4 months ago by sambioinfo20180
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Multimapping reads intervention in SNP calling
... Hi All, Hi, I have used bowtie2 (default settings) to align the reads to the reference genome. Due to presence of homoeologous genes in plant genome, there is a possibility of getting lots of multimapping reads and this might or will hinder while calculating SNPs. So i tried to remove the secondary ...
alignment samtools snp mpileup written 4 months ago by sambioinfo20180 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: To calculate the length of aligned genome
... Thanks Bastien. Is this the command to do so: `bedtools genomecov -ibam bamfile.bam -bga -g genomelength.txt` ...
written 6 months ago by sambioinfo20180
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To calculate the length of aligned genome
... Dear All, I have a bam file aligned to a reference genome. I would like to know if there is a way to calculate the over all length of aligned genome. Thanks in advance. Sam. ...
next-gen written 6 months ago by sambioinfo20180 • updated 6 months ago by Bastien Hervé3.9k
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Comment: C: Consensus sequence with characters apart from ATGC
... Thanks Fin for your help! ...
written 7 months ago by sambioinfo20180

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