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Recent Replies
Comment: Percentage coverage of reference genome by de novo genome
by
Lemonhope
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Thank you, I'll check out Quast!
Answer: How do I change the title font size in ViolinPlot (Seurat)
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Looking at the source code of the function it seems that they make individual plots with ggplot when `features` is `> 1` and then use patch…
Comment: Percentage coverage of reference genome by de novo genome
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Lemonhope
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Thank you for the response
to answer you question, no, the ddRADseq data (short paired end illumina reads) for all the samples were used …
Comment: Percentage coverage of reference genome by de novo genome
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Michael
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minimap2 can do this too, mummer (nucmer) is more accurate but slightly slower. If you want to do this as part of generating assembly stati…
Comment: TFs and Gene databases
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ijarne
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Thank you so much @jaredandrews07 it looks like I will be able to get what I intended with these sources !!
Comment: Percentage coverage of reference genome by de novo genome
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Joe
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If you have contigs for assemblies, using read-based approaches like samtools is probably not the way to go.
As you're interested in % cov…
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Has data been generated in the same batch, so same day, in the same 10x runs?
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So I am assuming you have calculated a Burrows-Wheeler transform, then add the FM-index for the first and last column of the BW-matrix. I r…
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I already told them but they couldn't come up with a useful solution :/
Comment: A question about reference genome for creating the consensus sequence
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ATpoint
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You aligned your data, that is your reference genome to compare against. If you want to change reference then realign.
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The vignette I followed, although lacking, seems better since it focuses on doing iterative process. I'll keep looking perhaps I'll find so…
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Hi, yes, my cram files cover the whole genome, which is actually individual genome information. I wonder how to adjust the base genome. Tha…
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At least according to the documentation, it seems for WGS you can use the `batch --method wgs` option. There is more information here: [htt…
Answer: A question about reference genome for creating the consensus sequence
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It is the consensus for all reads that overlap a given base, it's not a genome consensus unless your reads cover the entire genome.
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Hello everyone, I need to call the CNV from my hunam WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am tr…
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