User: BioGeek

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BioGeek130
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Posts by BioGeek

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Comment: C: How to extract all ONT reads that connect/overlaps two or more contigs ?
... mapping is done by minimap2 ...
written 10 weeks ago by BioGeek130
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How to extract all ONT reads that connect/overlaps two or more contigs ?
... I want to focus on all those reads that connect two or more contigs. How to extract ONLY those nanopore reads ? ...
reads nanopore scaffolding overlaps written 10 weeks ago by BioGeek130
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Comment: C: How to plot overlapping fragments in Circos ?
... from to value 1 VH1 JH1 88 2 VH3 JH1 273 3 VH4 JH1 10 4 VH5 JH1 0 5 VH6 JH1 0 6 VH1 JH2 43 7 VH3 JH2 113 8 VH4 JH2 153 9 VH5 JH2 0 10 VH6 JH2 50 11 VH1 JH3 226 12 VH3 JH3 432 13 VH4 JH ...
written 3 months ago by BioGeek130
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Answer: A: How to plot overlapping fragments in Circos ?
... Thanks for the script. I wanted to plot multiple hits scenarios, where single reference fragment/block is mapped to multiple locations in target. As shown above, h1 fragments have multiple hits on q1 and q2. I tried with your suggested script, but fail miserably :( ...
written 3 months ago by BioGeek130
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How to plot overlapping fragments in Circos ?
... ![enter image description here][1] How to Plot a circular overlapping plots, as shown in pic. ? I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/ data C D A 7 18 B 5 15 and it return http://mkweb.bcgsc.ca/tableviewer/tmp/fvufmlm/results/circos-table-fvufmlm-larg ...
circos plots overlaps written 3 months ago by BioGeek130
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How to present mapping result ?
... I usually do samtools flagstat to represent the mapping stats. Is there any best way to represent/present the mapping quality/results in details. ...
result mapping written 3 months ago by BioGeek130 • updated 3 months ago by michael.ante2.5k
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How to remove split/broken reads from bam file
... Is there any flag to remove broken (ONT reads split and map to different locations) reads from bam file. Note: The ONT reads mapped with gap should not remove. ...
minimap2 graphmap samtools split nanopore written 3 months ago by BioGeek130 • updated 3 months ago by Macspider2.4k
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Does MIRA do the phasing ?
... I notice many of the scientist using MIRA to assemble diploid and polyploid genomes (despite of warning by the author). I am just wondering, does the MIRA intelligent enough to phase? I suspect, it only produces haploid set of the genome ... Am I right ? ...
genome assembly ngs mira sequencing written 6 months ago by BioGeek130
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Comment: C: Remove duplicates reads Ids
... $ dedupe.sh in1=see.R1.fq in2=see.R2.fq out1=tt.R1.fq out2=tt.R2.fq [] java -Djava.library.path=/home/Tools/bbmap/jni/ -ea -Xmx200291m -Xms200291m -cp /home/Tools/bbmap/current/ jgi.Dedupe in1=see.R1.fq in2=see.R2.fq out1=tt.R1.fq out2=tt.R2.fq Executing jgi.Dedupe [in1=see.R1.f ...
written 12 months ago by BioGeek130
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Answer: A: Remove duplicates reads Ids
... #!/usr/bin/perl-w use strict; use warnings; my %id2seq=(); my $key = ''; $/ = '@HISEQ'; my $add='@HISEQ'; while(<>){ chomp; my ($defLine, @seqLines) = split /\n/, $_; my $sequence = join("\n",@seqLines); $id2seq{$defL ...
written 12 months ago by BioGeek130

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Student 14 months ago, asked a question with at least 3 up-votes. For How to differentiate between "horizontal gene transfer" and "contamination" in NGS data?

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