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I've been working on running mummer from within a script (for #144) and it would be super nice if future versions of mummer could read gzipped files without me having to uncompress them first -- e.g. …
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Hi
I recently found your manuscript and simGBS. I was looking for a GBS read simulator because I wanted to simulate GBS data from polyploids. I.e., take different genomes, simulate reads, mix them,…
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Hi developer,
I just want to make sure I am on the right track to make my own index. Because repbase is not openable, I downloaded the fasta file from GENCODE (Genome sequence, primary assembly (GR…
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In the example given in your document, the data used was a human genome. Can SNPRelate be used to analysis Plasmodium falciparum snp data as well?
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Hi,
I am using RepeatMasker to get L1 families in the reference genome
"RepeatMasker GCF.fa"
While I got a lof of L1 in the .out file, the size from 50bp-5k, I want to classfy subfamily of L1 by Re…
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Dear Professor Zhang,
The species I study is an insect which has 36 chromosomes,and its genome size is 5.6Gb. The initial genome was mounted to 40 chromosomes using Allhic software(Because the size o…
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(1) What method does unicycler use to determine the “circular” of contigs?
(2) Is it only for the contigs to be judged separately?
For example, I use unicycler to assemble 5 contigs (1, 2, 3, 4,…
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Users have emailed with problems using bam, only to find out that they are using e.g. bacterial bam files. If we are really requiring users to have human genomes, could we perform a quick check to see…
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@andrewrobertjones @timosachsenberg @jgriss :
We have an ongoing project to map the Genome coordinates into ESENBML, we have been doing this for a while. Internally, PRIDE has moved into mztab lon…
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The reason multiple insert libraries are used is to strike a balance between long and short range information. Long-insert mate pair libraries are great at telling you two contigs are linked but doesn…