User: sambioinfo2018

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Posts by sambioinfo2018

<prev • 29 results • page 1 of 3 • next >
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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 26 days ago by sambioinfo20180 • updated 26 days ago by genomax60k
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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 29 days 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 29 days ago by sambioinfo20180 • updated 10 days 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 3 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 3 months ago by sambioinfo20180 • updated 3 months ago by Bastien Hervé2.8k
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Comment: C: Consensus sequence with characters apart from ATGC
... Thanks Fin for your help! ...
written 4 months ago by sambioinfo20180
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Comment: C: Consensus sequence with characters apart from ATGC
... Or do you have the better way to do the same? ...
written 4 months ago by sambioinfo20180
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Comment: C: Consensus sequence with characters apart from ATGC
... Thanks finswimmer. i am using samtools v1.8 and bcftools v1.8. So should i use the following command to generate the consensus sequence: bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Oz -o calls.vcf.gz tabix calls.vcf.gz cat reference.fa | bcftools consensus ...
written 4 months ago by sambioinfo20180
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Comment: C: Consensus sequence with characters apart from ATGC
... Thanks Bastien for your reply. But why is base quality printed in a consensus fasta file. I would like to use this fasta file for further analysis. ...
written 4 months ago by sambioinfo20180
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Consensus sequence with characters apart from ATGC
... Dear All, I have aligned the reads to the reference genome using Bowtie2. The generated sam was then converted to bam and sorted. The sorted file using the following command i tried to generate consensus sequence: samtools mpileup -uf ref.fa aligned_sorted.bam | bcftools call -c | vcfutils.pl ...
next-gen written 4 months ago by sambioinfo20180 • updated 4 months ago by finswimmer8.9k

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