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User: mictadlo

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mictadlo0
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Posts by mictadlo

<prev • 58 results • page 1 of 6 • next >
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genetic and linkage maps construction
... Hello, We have one population consisted of 192 F3 lines resulting from a cross between two plant genomes. All our GBS reads are stored in two folders (96 files in each). 1740-44-01> ls -1 *.gz 10_S0_L001_R1_001.fastq.gz 10_S0_L001_R2_001.fastq.gz 11_S0_L001_R1_001.fastq.gz ...
snp genetic map linkage maps assembly gbs written 22 days ago by mictadlo0
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vcf to venn diagram
... Hi, I created VCF files for 5 cultivars in the following way: bcftools mpileup -Ou -f $2 ${1}/all.sorted.dedup.bam | bcftools call -mv -Ob -o ${1}/calls.bcf bcftools view -i '%QUAL>=20' ${1}/calls.bcf > ${1}/calls-gt-q20.vcf How can I create a venn-diagram out of those files? Thank you in ...
vcf snps venn diagram ggplot2 written 7 weeks ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... I used [HiCExplorer](https://academic.oup.com/nar/article/46/W1/W11/5036837) with help of [snakePipes](https://www.biorxiv.org/content/early/2018/09/04/407312). Do you think that HiCExplorer's output could help to get chromosome groups? ...
written 9 weeks ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... Our goal is to scaffold our 4000 contings into 19 scaffolds/chromosomes with help of HiC data. Similar to [this](https://www.nature.com/articles/s41438-017-0013-y/figures/1). Unfortunately, LACHESIS is not working on our cluster and therefore I am looking for alternatives. ...
written 9 weeks ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... Does those anchors would allow me to extract for each chromosomes a FASTA file e.g. we expecting to get 19 chromosomes so we would like to get 19 FASTA files? Do you have any code examples? ...
written 9 weeks ago by mictadlo0
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Comment: C: from denove contig assembly to chromosome bins
... How is it possible to extract chromosome bins out of `ContactMatrix`? ...
written 9 weeks ago by mictadlo0
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from denove contig assembly to chromosome bins
... Hi, By any chance, do anyone have any recommendations which software could provide me with chromosome bins from a denovo contig assembly by using HiC data and without any annotation? Thank you in advance. ...
gothic diffhic hic hic-c hicup written 9 weeks ago by mictadlo0 • updated 9 weeks ago by Aaron Lun22k
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plot get overridden rather to overlapped
... I have the below code. Which executes twice a plot_denisities function. Unfortunately, when I execute this function again it plots a completely new picture rather overlap the two plots into one plot. #install if necessary source("http://bioconductor.org/biocLite.R") biocLite("Rsamtools" ...
rsamtools plot ggplot2 written 10 weeks ago by mictadlo0 • updated 10 weeks ago by James W. MacDonald49k
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Answer: C: Error in scanBam(bam_fn) : could not find function "scanBam"
... Solution was to do apt update && apt install zlib1g-dev ...
written 10 weeks ago by mictadlo0
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Error in scanBam(bam_fn) : could not find function "scanBam"
... Hi, By any chance, do anyone have any recommendations which software could provide me with chromosome bins from a denovo contig assembly by using HiC data and without any annotation? Thank you in advance. ...
gothic diffhic hic hic-c hicup written 10 weeks ago by mictadlo0

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Popular Question 16 months ago, created a question with more than 1,000 views. For Error in plot.new() : figure margins too large

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