User: BAGeno

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BAGeno20
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Posts by BAGeno

<prev • 17 results • page 1 of 2 • next >
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Comparing rsids in two VCF
... Hi I have two VCF and I want to find common rsids in those two files. For this purpose I have used grep command by taking list of rsids from one file and running it on other file, but it gave me some extra rsids as well which were not present in the list. I have also used bcftools isec command but ...
vcf rsid written 22 days ago by BAGeno20 • updated 22 days ago by Pierre Lindenbaum95k
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Difference between read and contig based taxonomic classification
... Hi, I want to understand the difference between read based and contig based classification. What is the methodology behind these two? Which is more accurate? ...
reads classification contigs taxonomic written 26 days ago by BAGeno20 • updated 8 days ago by Sej Modha1.3k
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Comment: C: GC content and average fold coverage of contigs
... I am trying to understand a graph. this graph is plotted between % GC content and average fold coverage. Some point on the graph has low % GC content but high fold coverage and vice versa. I am trying to understand what this means.![Here is its link][1] [1]: https://s17.postimg.org/3v9k1kpvz/Con ...
written 26 days ago by BAGeno20
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Comment: C: GC content and average fold coverage of contigs
... If there is other way around meaning low GC content but high fold coverage? ...
written 26 days ago by BAGeno20
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GC content and average fold coverage of contigs
... Hi, I want to know what is the relation between GC content and average fold coverage of contigs? If we have high percentage of GC content but low coverage of contigs what that means? ...
genome gc content fold coverage written 26 days ago by BAGeno20
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Merged RsIDs in different files
... Hi I want to check rsIDs present in my VCF in different databsase to know whether these variants are present in certain disease condition or not. But problem I am facing is of merged rsIDs as there can be different rsIDs on same position. I fear that there can be a variant which have different rsID ...
vcf rsids database written 4 weeks ago by BAGeno20
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Comment: C: Grep Position List
... It worked :) Thank you ...
written 4 weeks ago by BAGeno20
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Comment: C: Grep Position List
... This is what myNew.vcf look like. ##bcftools_filterCommand=filter -i DP>=20 myNew.raw30.vcf ##bcftools_filterCommand=filter -i GQ>=30 New.DP20.vcf ##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/) ##liftOverTime=April01,2017 #CHROM POS ID REF ...
written 4 weeks ago by BAGeno20
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Comment: C: Grep Position List
... This is giving VCF file with just header. ...
written 4 weeks ago by BAGeno20
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Comment: C: Grep Position List
... I tried this command but it did not work. vcftools --vcf myNew.vcf --positions Chr.pos.tsv --out Filtered_File ...
written 4 weeks ago by BAGeno20

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