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Recent Replies
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements?
by
cmdcolin
★
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i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations
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Jordan M Eizenga
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If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ?
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You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ?
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I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data
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Tm
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I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too?
We tried using Q…
Comment: Problematic fastq files...How can we trust them?
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I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download
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cmdcolin
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----------
some common ones include
1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
…
Comment: GO categorization
by
m.habib
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Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
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jv
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I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
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And the hg38 version can be found here:
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz
And for convenience, upda…
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You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ?
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Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
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Hello,
I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters:
./clumpify.sh in1=$d…
Comment: Problematic fastq files...How can we trust them?
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perhaps ask her about the origin of the data, how was the data postprocessed
FASTQ data is a bit more resilient than other types of data a…
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If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes.
Basically your …
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